Package 'RSirius'

Description

Simple object to hold account credentials, e.g. to perform login operations. If refreshToken is given, it is usually preferred over password based authentication. But in the end this is up to the respective web service.

AccountCredentials Class

Format

An R6Class generator object

Details

Create a new AccountCredentials

Public fields

Methods

Public methods

• AccountCredentials$new()

• AccountCredentials$toJSON()

• AccountCredentials$toList()

• AccountCredentials$toSimpleType()

• AccountCredentials$fromJSON()

• AccountCredentials$toJSONString()

• AccountCredentials$fromJSONString()

• AccountCredentials$validateJSON()

• AccountCredentials$toString()

• AccountCredentials$isValid()

• AccountCredentials$getInvalidFields()

• AccountCredentials$print()

• AccountCredentials$clone()

Method new()

Initialize a new AccountCredentials class.

Usage

AccountCredentials$new(
  username = NULL,
  password = NULL,
  refreshToken = NULL,
  ...
)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

AccountCredentials$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

AccountCredentials$toList()

Returns

AccountCredentials as a base R list.

Examples

# convert array of AccountCredentials (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert AccountCredentials to a base R type

Usage

AccountCredentials$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of AccountCredentials

Usage

AccountCredentials$fromJSON(input_json)

Arguments

Returns

the instance of AccountCredentials

Method toJSONString()

To JSON String

Usage

AccountCredentials$toJSONString(...)

Arguments

Returns

AccountCredentials in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of AccountCredentials

Usage

AccountCredentials$fromJSONString(input_json)

Arguments

Returns

the instance of AccountCredentials

Method validateJSON()

Validate JSON input with respect to AccountCredentials and throw an exception if invalid

Usage

AccountCredentials$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

AccountCredentials$toString()

Returns

String representation of AccountCredentials

Method isValid()

Return true if the values in all fields are valid.

Usage

AccountCredentials$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

AccountCredentials$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

AccountCredentials$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

AccountCredentials$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `AccountCredentials$toList`
## ------------------------------------------------

# convert array of AccountCredentials (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

AccountInfo Class

AccountInfo Class

Format

An R6Class generator object

Details

Create a new AccountInfo

Public fields

Methods

Public methods

• AccountInfo$new()

• AccountInfo$toJSON()

• AccountInfo$toList()

• AccountInfo$toSimpleType()

• AccountInfo$fromJSON()

• AccountInfo$toJSONString()

• AccountInfo$fromJSONString()

• AccountInfo$validateJSON()

• AccountInfo$toString()

• AccountInfo$isValid()

• AccountInfo$getInvalidFields()

• AccountInfo$print()

• AccountInfo$clone()

Method new()

Initialize a new AccountInfo class.

Usage

AccountInfo$new(
  userID = NULL,
  username = NULL,
  userEmail = NULL,
  gravatarURL = NULL,
  subscriptions = NULL,
  activeSubscriptionId = NULL,
  ...
)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

AccountInfo$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

AccountInfo$toList()

Returns

AccountInfo as a base R list.

Examples

# convert array of AccountInfo (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert AccountInfo to a base R type

Usage

AccountInfo$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of AccountInfo

Usage

AccountInfo$fromJSON(input_json)

Arguments

Returns

the instance of AccountInfo

Method toJSONString()

To JSON String

Usage

AccountInfo$toJSONString(...)

Arguments

Returns

AccountInfo in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of AccountInfo

Usage

AccountInfo$fromJSONString(input_json)

Arguments

Returns

the instance of AccountInfo

Method validateJSON()

Validate JSON input with respect to AccountInfo and throw an exception if invalid

Usage

AccountInfo$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

AccountInfo$toString()

Returns

String representation of AccountInfo

Method isValid()

Return true if the values in all fields are valid.

Usage

AccountInfo$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

AccountInfo$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

AccountInfo$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

AccountInfo$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `AccountInfo$toList`
## ------------------------------------------------

# convert array of AccountInfo (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

ActuatorApi

Format

An R6Class generator object

Details

SIRIUS Nightsky API

REST API that provides the full functionality of SIRIUS and its web services as background service. It is intended as entry-point for scripting languages and software integration SDKs.This API is exposed by SIRIUS 6

The version of the OpenAPI document: 3.2 Generated by: https://openapi-generator.tech

Public fields

Methods

Public methods

• ActuatorApi$new()

• ActuatorApi$Health()

• ActuatorApi$HealthWithHttpInfo()

• ActuatorApi$Shutdown()

• ActuatorApi$ShutdownWithHttpInfo()

• ActuatorApi$clone()

Method new()

Initialize a new ActuatorApi.

Usage

ActuatorApi$new(api_client)

Arguments

Method Health()

Actuator web endpoint 'health'

Usage

ActuatorApi$Health(data_file = NULL, ...)

Arguments

Returns

object

Method HealthWithHttpInfo()

Actuator web endpoint 'health'

Usage

ActuatorApi$HealthWithHttpInfo(data_file = NULL, ...)

Arguments

Returns

API response (object) with additional information such as HTTP status code, headers

Method Shutdown()

Actuator web endpoint 'shutdown'

Usage

ActuatorApi$Shutdown(...)

Arguments

Returns

void

Method ShutdownWithHttpInfo()

Actuator web endpoint 'shutdown'

Usage

ActuatorApi$ShutdownWithHttpInfo(...)

Arguments

Returns

API response (void) with additional information such as HTTP status code, headers

Method clone()

The objects of this class are cloneable with this method.

Usage

ActuatorApi$clone(deep = FALSE)

Arguments

Examples

## Not run: 
####################  Health  ####################

library(RSirius)

#Actuator web endpoint 'health'
api_instance <- rsirius_api$new()

# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$Health(data_file = "result.txt")
result <- api_instance$actuator_api$Health()
dput(result)


####################  Shutdown  ####################

library(RSirius)

#Actuator web endpoint 'shutdown'
api_instance <- rsirius_api$new()

api_instance$actuator_api$Shutdown()



## End(Not run)

Description

The AlignedFeature contains the ID of a feature (aligned over runs) together with some read-only information that might be displayed in some summary view.

AlignedFeature Class

Format

An R6Class generator object

Details

Create a new AlignedFeature

Public fields

Methods

Public methods

• AlignedFeature$new()

• AlignedFeature$toJSON()

• AlignedFeature$toList()

• AlignedFeature$toSimpleType()

• AlignedFeature$fromJSON()

• AlignedFeature$toJSONString()

• AlignedFeature$fromJSONString()

• AlignedFeature$validateJSON()

• AlignedFeature$toString()

• AlignedFeature$isValid()

• AlignedFeature$getInvalidFields()

• AlignedFeature$print()

• AlignedFeature$clone()

Method new()

Initialize a new AlignedFeature class.

Usage

AlignedFeature$new(
  charge,
  detectedAdducts,
  alignedFeatureId = NULL,
  compoundId = NULL,
  name = NULL,
  externalFeatureId = NULL,
  ionMass = NULL,
  rtStartSeconds = NULL,
  rtEndSeconds = NULL,
  rtApexSeconds = NULL,
  quality = NULL,
  hasMs1 = NULL,
  hasMsMs = NULL,
  msData = NULL,
  topAnnotations = NULL,
  topAnnotationsDeNovo = NULL,
  computing = NULL,
  computedTools = NULL,
  qualities = NULL,
  tags = NULL,
  ...
)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

AlignedFeature$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

AlignedFeature$toList()

Returns

AlignedFeature as a base R list.

Examples

# convert array of AlignedFeature (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert AlignedFeature to a base R type

Usage

AlignedFeature$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of AlignedFeature

Usage

AlignedFeature$fromJSON(input_json)

Arguments

Returns

the instance of AlignedFeature

Method toJSONString()

To JSON String

Usage

AlignedFeature$toJSONString(...)

Arguments

Returns

AlignedFeature in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of AlignedFeature

Usage

AlignedFeature$fromJSONString(input_json)

Arguments

Returns

the instance of AlignedFeature

Method validateJSON()

Validate JSON input with respect to AlignedFeature and throw an exception if invalid

Usage

AlignedFeature$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

AlignedFeature$toString()

Returns

String representation of AlignedFeature

Method isValid()

Return true if the values in all fields are valid.

Usage

AlignedFeature$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

AlignedFeature$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

AlignedFeature$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

AlignedFeature$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `AlignedFeature$toList`
## ------------------------------------------------

# convert array of AlignedFeature (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

AllowedFeatures Class

AllowedFeatures Class

Format

An R6Class generator object

Details

Create a new AllowedFeatures

Public fields

Methods

Public methods

• AllowedFeatures$new()

• AllowedFeatures$toJSON()

• AllowedFeatures$toList()

• AllowedFeatures$toSimpleType()

• AllowedFeatures$fromJSON()

• AllowedFeatures$toJSONString()

• AllowedFeatures$fromJSONString()

• AllowedFeatures$validateJSON()

• AllowedFeatures$toString()

• AllowedFeatures$isValid()

• AllowedFeatures$getInvalidFields()

• AllowedFeatures$print()

• AllowedFeatures$clone()

Method new()

Initialize a new AllowedFeatures class.

Usage

AllowedFeatures$new(
  cli = NULL,
  api = NULL,
  deNovo = NULL,
  importMSRuns = NULL,
  importPeakLists = NULL,
  importCef = NULL,
  transformationProducts = NULL,
  ...
)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

AllowedFeatures$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

AllowedFeatures$toList()

Returns

AllowedFeatures as a base R list.

Examples

# convert array of AllowedFeatures (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert AllowedFeatures to a base R type

Usage

AllowedFeatures$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of AllowedFeatures

Usage

AllowedFeatures$fromJSON(input_json)

Arguments

Returns

the instance of AllowedFeatures

Method toJSONString()

To JSON String

Usage

AllowedFeatures$toJSONString(...)

Arguments

Returns

AllowedFeatures in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of AllowedFeatures

Usage

AllowedFeatures$fromJSONString(input_json)

Arguments

Returns

the instance of AllowedFeatures

Method validateJSON()

Validate JSON input with respect to AllowedFeatures and throw an exception if invalid

Usage

AllowedFeatures$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

AllowedFeatures$toString()

Returns

String representation of AllowedFeatures

Method isValid()

Return true if the values in all fields are valid.

Usage

AllowedFeatures$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

AllowedFeatures$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

AllowedFeatures$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

AllowedFeatures$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `AllowedFeatures$toList`
## ------------------------------------------------

# convert array of AllowedFeatures (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

AnnotatedMsMsData Class

AnnotatedMsMsData Class

Format

An R6Class generator object

Details

Create a new AnnotatedMsMsData

Public fields

Methods

Public methods

• AnnotatedMsMsData$new()

• AnnotatedMsMsData$toJSON()

• AnnotatedMsMsData$toList()

• AnnotatedMsMsData$toSimpleType()

• AnnotatedMsMsData$fromJSON()

• AnnotatedMsMsData$toJSONString()

• AnnotatedMsMsData$fromJSONString()

• AnnotatedMsMsData$validateJSON()

• AnnotatedMsMsData$toString()

• AnnotatedMsMsData$isValid()

• AnnotatedMsMsData$getInvalidFields()

• AnnotatedMsMsData$print()

• AnnotatedMsMsData$clone()

Method new()

Initialize a new AnnotatedMsMsData class.

Usage

AnnotatedMsMsData$new(mergedMs2, ms2Spectra, ...)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

AnnotatedMsMsData$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

AnnotatedMsMsData$toList()

Returns

AnnotatedMsMsData as a base R list.

Examples

# convert array of AnnotatedMsMsData (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert AnnotatedMsMsData to a base R type

Usage

AnnotatedMsMsData$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of AnnotatedMsMsData

Usage

AnnotatedMsMsData$fromJSON(input_json)

Arguments

Returns

the instance of AnnotatedMsMsData

Method toJSONString()

To JSON String

Usage

AnnotatedMsMsData$toJSONString(...)

Arguments

Returns

AnnotatedMsMsData in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of AnnotatedMsMsData

Usage

AnnotatedMsMsData$fromJSONString(input_json)

Arguments

Returns

the instance of AnnotatedMsMsData

Method validateJSON()

Validate JSON input with respect to AnnotatedMsMsData and throw an exception if invalid

Usage

AnnotatedMsMsData$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

AnnotatedMsMsData$toString()

Returns

String representation of AnnotatedMsMsData

Method isValid()

Return true if the values in all fields are valid.

Usage

AnnotatedMsMsData$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

AnnotatedMsMsData$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

AnnotatedMsMsData$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

AnnotatedMsMsData$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `AnnotatedMsMsData$toList`
## ------------------------------------------------

# convert array of AnnotatedMsMsData (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

AnnotatedPeak Class

AnnotatedPeak Class

Format

An R6Class generator object

Details

Create a new AnnotatedPeak

Public fields

Methods

Public methods

• AnnotatedPeak$new()

• AnnotatedPeak$toJSON()

• AnnotatedPeak$toList()

• AnnotatedPeak$toSimpleType()

• AnnotatedPeak$fromJSON()

• AnnotatedPeak$toJSONString()

• AnnotatedPeak$fromJSONString()

• AnnotatedPeak$validateJSON()

• AnnotatedPeak$toString()

• AnnotatedPeak$isValid()

• AnnotatedPeak$getInvalidFields()

• AnnotatedPeak$print()

• AnnotatedPeak$clone()

Method new()

Initialize a new AnnotatedPeak class.

Usage

AnnotatedPeak$new(mz = NULL, intensity = NULL, peakAnnotation = NULL, ...)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

AnnotatedPeak$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

AnnotatedPeak$toList()

Returns

AnnotatedPeak as a base R list.

Examples

# convert array of AnnotatedPeak (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert AnnotatedPeak to a base R type

Usage

AnnotatedPeak$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of AnnotatedPeak

Usage

AnnotatedPeak$fromJSON(input_json)

Arguments

Returns

the instance of AnnotatedPeak

Method toJSONString()

To JSON String

Usage

AnnotatedPeak$toJSONString(...)

Arguments

Returns

AnnotatedPeak in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of AnnotatedPeak

Usage

AnnotatedPeak$fromJSONString(input_json)

Arguments

Returns

the instance of AnnotatedPeak

Method validateJSON()

Validate JSON input with respect to AnnotatedPeak and throw an exception if invalid

Usage

AnnotatedPeak$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

AnnotatedPeak$toString()

Returns

String representation of AnnotatedPeak

Method isValid()

Return true if the values in all fields are valid.

Usage

AnnotatedPeak$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

AnnotatedPeak$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

AnnotatedPeak$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

AnnotatedPeak$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `AnnotatedPeak$toList`
## ------------------------------------------------

# convert array of AnnotatedPeak (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

Spectrum model with peak annotations based on the fragmentation tree and Epimetheus substructure annotations. Molecular formula and adduct of the spectrum are identical to the ones of the corresponding molecular formula candidate and FragmentationTree. Fragment molecular formulas and adducts correspond to the FragmentationTree's FragmentNodes

AnnotatedSpectrum Class

Format

An R6Class generator object

Details

Create a new AnnotatedSpectrum

Public fields

Methods

Public methods

• AnnotatedSpectrum$new()

• AnnotatedSpectrum$toJSON()

• AnnotatedSpectrum$toList()

• AnnotatedSpectrum$toSimpleType()

• AnnotatedSpectrum$fromJSON()

• AnnotatedSpectrum$toJSONString()

• AnnotatedSpectrum$fromJSONString()

• AnnotatedSpectrum$validateJSON()

• AnnotatedSpectrum$toString()

• AnnotatedSpectrum$isValid()

• AnnotatedSpectrum$getInvalidFields()

• AnnotatedSpectrum$print()

• AnnotatedSpectrum$clone()

Method new()

Initialize a new AnnotatedSpectrum class.

Usage

AnnotatedSpectrum$new(
  cosineQuery,
  peaks,
  name = NULL,
  msLevel = NULL,
  collisionEnergy = NULL,
  instrument = NULL,
  precursorMz = NULL,
  scanNumber = NULL,
  precursorPeak = NULL,
  absIntensityFactor = NULL,
  maxNormFactor = NULL,
  sumNormFactor = NULL,
  l2NormFactor = NULL,
  firstPeakNormFactor = NULL,
  spectrumAnnotation = NULL,
  ...
)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

AnnotatedSpectrum$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

AnnotatedSpectrum$toList()

Returns

AnnotatedSpectrum as a base R list.

Examples

# convert array of AnnotatedSpectrum (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert AnnotatedSpectrum to a base R type

Usage

AnnotatedSpectrum$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of AnnotatedSpectrum

Usage

AnnotatedSpectrum$fromJSON(input_json)

Arguments

Returns

the instance of AnnotatedSpectrum

Method toJSONString()

To JSON String

Usage

AnnotatedSpectrum$toJSONString(...)

Arguments

Returns

AnnotatedSpectrum in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of AnnotatedSpectrum

Usage

AnnotatedSpectrum$fromJSONString(input_json)

Arguments

Returns

the instance of AnnotatedSpectrum

Method validateJSON()

Validate JSON input with respect to AnnotatedSpectrum and throw an exception if invalid

Usage

AnnotatedSpectrum$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

AnnotatedSpectrum$toString()

Returns

String representation of AnnotatedSpectrum

Method isValid()

Return true if the values in all fields are valid.

Usage

AnnotatedSpectrum$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

AnnotatedSpectrum$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

AnnotatedSpectrum$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

AnnotatedSpectrum$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `AnnotatedSpectrum$toList`
## ------------------------------------------------

# convert array of AnnotatedSpectrum (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

AnyValue Class

Format

An R6Class generator object

Public fields

Methods

Public methods

• AnyValue$new()

• AnyValue$fromJSONString()

• AnyValue$fromJSON()

• AnyValue$toJSONString()

• AnyValue$toJSON()

• AnyValue$validateJSON()

• AnyValue$toString()

• AnyValue$print()

• AnyValue$clone()

Method new()

Initialize a new AnyValue.

Usage

AnyValue$new(instance = NULL)

Arguments

Method fromJSONString()

Deserialize JSON string into an instance of AnyValue. An alias to the method 'fromJSON'.

Usage

AnyValue$fromJSONString(input)

Arguments

Returns

An instance of AnyValue.

Method fromJSON()

Deserialize JSON string into an instance of AnyValue.

Usage

AnyValue$fromJSON(input)

Arguments

Returns

An instance of AnyValue.

Method toJSONString()

Serialize AnyValue to JSON string.

Usage

AnyValue$toJSONString()

Returns

JSON string representation of the AnyValue.

Method toJSON()

Serialize AnyValue to JSON.

Usage

AnyValue$toJSON()

Returns

JSON representation of the AnyValue.

Method validateJSON()

Validate the input JSON with respect to AnyValue and throw exception if invalid.

Usage

AnyValue$validateJSON(input)

Arguments

Method toString()

Returns the string representation of the instance.

Usage

AnyValue$toString()

Returns

The string representation of the instance.

Method print()

Print the object

Usage

AnyValue$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

AnyValue$clone(deep = FALSE)

Arguments

Description

ApiClient Class

Format

An R6Class generator object

Details

SIRIUS Nightsky API

REST API that provides the full functionality of SIRIUS and its web services as background service. It is intended as entry-point for scripting languages and software integration SDKs.This API is exposed by SIRIUS 6

The version of the OpenAPI document: 3.2 Generated by: https://openapi-generator.tech

ApiClient Class

Generic API client for OpenAPI client library builds. OpenAPI generic API client. This client handles the client- server communication, and is invariant across implementations. Specifics of the methods and models for each application are generated from the OpenAPI Generator templates.

NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech). Ref: https://openapi-generator.tech Do not edit the class manually.

Public fields

Methods

Public methods

• ApiClient$new()

• ApiClient$CallApi()

• ApiClient$Execute()

• ApiClient$deserialize()

• ApiClient$deserializeObj()

• ApiClient$select_header()

• ApiClient$clone()

Method new()

Initialize a new ApiClient.

Usage

ApiClient$new(
  base_path = NULL,
  user_agent = NULL,
  default_headers = NULL,
  username = NULL,
  password = NULL,
  api_keys = NULL,
  access_token = NULL,
  bearer_token = NULL,
  timeout = NULL,
  retry_status_codes = NULL,
  max_retry_attempts = NULL
)

Arguments

Method CallApi()

Prepare to make an API call with the retry logic.

Usage

ApiClient$CallApi(
  url,
  method,
  query_params,
  header_params,
  form_params,
  file_params,
  accepts,
  content_types,
  body,
  is_oauth = FALSE,
  oauth_scopes = NULL,
  stream_callback = NULL,
  ...
)

Arguments

Returns

HTTP response

Method Execute()

Make an API call

Usage

ApiClient$Execute(
  req,
  method,
  query_params,
  header_params,
  form_params,
  file_params,
  accepts,
  content_types,
  body,
  is_oauth = FALSE,
  oauth_scopes = NULL,
  stream_callback = NULL,
  ...
)

Arguments

Returns

HTTP response

Method deserialize()

Deserialize the content of API response to the given type.

Usage

ApiClient$deserialize(raw_response, return_type, pkg_env)

Arguments

Returns

Deserialized object.

Method deserializeObj()

Deserialize the response from jsonlite object based on the given type. by handling complex and nested types by iterating recursively Example return_types will be like "array[integer]", "map(Pet)", "array[map(Tag)]", etc.

Usage

ApiClient$deserializeObj(obj, return_type, pkg_env)

Arguments

Returns

Deserialized object.

Method select_header()

Return a property header (for accept or content-type). If JSON-related MIME is found, return it. Otherwise, return the first one, if any.

Usage

ApiClient$select_header(headers)

Arguments

Returns

A header (e.g. 'application/json')

Method clone()

The objects of this class are cloneable with this method.

Usage

ApiClient$clone(deep = FALSE)

Arguments

Description

ApiResponse Class

Format

An R6Class generator object

Details

SIRIUS Nightsky API

REST API that provides the full functionality of SIRIUS and its web services as background service. It is intended as entry-point for scripting languages and software integration SDKs.This API is exposed by SIRIUS 6

The version of the OpenAPI document: 3.2 Generated by: https://openapi-generator.tech

Public fields

Methods

Public methods

• ApiResponse$new()

• ApiResponse$response_as_text()

• ApiResponse$clone()

Method new()

Initialize a new ApiResponse class.

Usage

ApiResponse$new(
  content = NULL,
  response = NULL,
  status_code = NULL,
  status_code_desc = NULL,
  headers = NULL
)

Arguments

Method response_as_text()

The response is stored as a raw vector. Use this to access the response after converting it to text. If the response is not coercible to text NA is returned.

Usage

ApiResponse$response_as_text(from_encoding = "", to_encoding = "UTF-8")

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

ApiResponse$clone(deep = FALSE)

Arguments

Description

BackgroundComputationsStateEvent Class

BackgroundComputationsStateEvent Class

Format

An R6Class generator object

Details

Create a new BackgroundComputationsStateEvent

Public fields

Methods

Public methods

• BackgroundComputationsStateEvent$new()

• BackgroundComputationsStateEvent$toJSON()

• BackgroundComputationsStateEvent$toList()

• BackgroundComputationsStateEvent$toSimpleType()

• BackgroundComputationsStateEvent$fromJSON()

• BackgroundComputationsStateEvent$toJSONString()

• BackgroundComputationsStateEvent$fromJSONString()

• BackgroundComputationsStateEvent$validateJSON()

• BackgroundComputationsStateEvent$toString()

• BackgroundComputationsStateEvent$isValid()

• BackgroundComputationsStateEvent$getInvalidFields()

• BackgroundComputationsStateEvent$print()

• BackgroundComputationsStateEvent$clone()

Method new()

Initialize a new BackgroundComputationsStateEvent class.

Usage

BackgroundComputationsStateEvent$new(
  affectedJobs,
  numberOfJobs,
  numberOfRunningJobs,
  numberOfFinishedJobs,
  ...
)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

BackgroundComputationsStateEvent$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

BackgroundComputationsStateEvent$toList()

Returns

BackgroundComputationsStateEvent as a base R list.

Examples

# convert array of BackgroundComputationsStateEvent (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert BackgroundComputationsStateEvent to a base R type

Usage

BackgroundComputationsStateEvent$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of BackgroundComputationsStateEvent

Usage

BackgroundComputationsStateEvent$fromJSON(input_json)

Arguments

Returns

the instance of BackgroundComputationsStateEvent

Method toJSONString()

To JSON String

Usage

BackgroundComputationsStateEvent$toJSONString(...)

Arguments

Returns

BackgroundComputationsStateEvent in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of BackgroundComputationsStateEvent

Usage

BackgroundComputationsStateEvent$fromJSONString(input_json)

Arguments

Returns

the instance of BackgroundComputationsStateEvent

Method validateJSON()

Validate JSON input with respect to BackgroundComputationsStateEvent and throw an exception if invalid

Usage

BackgroundComputationsStateEvent$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

BackgroundComputationsStateEvent$toString()

Returns

String representation of BackgroundComputationsStateEvent

Method isValid()

Return true if the values in all fields are valid.

Usage

BackgroundComputationsStateEvent$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

BackgroundComputationsStateEvent$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

BackgroundComputationsStateEvent$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

BackgroundComputationsStateEvent$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `BackgroundComputationsStateEvent$toList`
## ------------------------------------------------

# convert array of BackgroundComputationsStateEvent (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

BasicSpectrum Class

BasicSpectrum Class

Format

An R6Class generator object

Details

Create a new BasicSpectrum

Public fields

Methods

Public methods

• BasicSpectrum$new()

• BasicSpectrum$toJSON()

• BasicSpectrum$toList()

• BasicSpectrum$toSimpleType()

• BasicSpectrum$fromJSON()

• BasicSpectrum$toJSONString()

• BasicSpectrum$fromJSONString()

• BasicSpectrum$validateJSON()

• BasicSpectrum$toString()

• BasicSpectrum$isValid()

• BasicSpectrum$getInvalidFields()

• BasicSpectrum$print()

• BasicSpectrum$clone()

Method new()

Initialize a new BasicSpectrum class.

Usage

BasicSpectrum$new(
  cosineQuery,
  peaks,
  name = NULL,
  msLevel = NULL,
  collisionEnergy = NULL,
  instrument = NULL,
  precursorMz = NULL,
  scanNumber = NULL,
  precursorPeak = NULL,
  absIntensityFactor = NULL,
  maxNormFactor = NULL,
  sumNormFactor = NULL,
  l2NormFactor = NULL,
  firstPeakNormFactor = NULL,
  ...
)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

BasicSpectrum$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

BasicSpectrum$toList()

Returns

BasicSpectrum as a base R list.

Examples

# convert array of BasicSpectrum (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert BasicSpectrum to a base R type

Usage

BasicSpectrum$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of BasicSpectrum

Usage

BasicSpectrum$fromJSON(input_json)

Arguments

Returns

the instance of BasicSpectrum

Method toJSONString()

To JSON String

Usage

BasicSpectrum$toJSONString(...)

Arguments

Returns

BasicSpectrum in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of BasicSpectrum

Usage

BasicSpectrum$fromJSONString(input_json)

Arguments

Returns

the instance of BasicSpectrum

Method validateJSON()

Validate JSON input with respect to BasicSpectrum and throw an exception if invalid

Usage

BasicSpectrum$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

BasicSpectrum$toString()

Returns

String representation of BasicSpectrum

Method isValid()

Return true if the values in all fields are valid.

Usage

BasicSpectrum$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

BasicSpectrum$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

BasicSpectrum$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

BasicSpectrum$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `BasicSpectrum$toList`
## ------------------------------------------------

# convert array of BasicSpectrum (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

BinaryFingerprint Class

BinaryFingerprint Class

Format

An R6Class generator object

Details

Create a new BinaryFingerprint

Public fields

Methods

Public methods

• BinaryFingerprint$new()

• BinaryFingerprint$toJSON()

• BinaryFingerprint$toList()

• BinaryFingerprint$toSimpleType()

• BinaryFingerprint$fromJSON()

• BinaryFingerprint$toJSONString()

• BinaryFingerprint$fromJSONString()

• BinaryFingerprint$validateJSON()

• BinaryFingerprint$toString()

• BinaryFingerprint$isValid()

• BinaryFingerprint$getInvalidFields()

• BinaryFingerprint$print()

• BinaryFingerprint$clone()

Method new()

Initialize a new BinaryFingerprint class.

Usage

BinaryFingerprint$new(bitsSet = NULL, length = NULL, ...)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

BinaryFingerprint$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

BinaryFingerprint$toList()

Returns

BinaryFingerprint as a base R list.

Examples

# convert array of BinaryFingerprint (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert BinaryFingerprint to a base R type

Usage

BinaryFingerprint$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of BinaryFingerprint

Usage

BinaryFingerprint$fromJSON(input_json)

Arguments

Returns

the instance of BinaryFingerprint

Method toJSONString()

To JSON String

Usage

BinaryFingerprint$toJSONString(...)

Arguments

Returns

BinaryFingerprint in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of BinaryFingerprint

Usage

BinaryFingerprint$fromJSONString(input_json)

Arguments

Returns

the instance of BinaryFingerprint

Method validateJSON()

Validate JSON input with respect to BinaryFingerprint and throw an exception if invalid

Usage

BinaryFingerprint$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

BinaryFingerprint$toString()

Returns

String representation of BinaryFingerprint

Method isValid()

Return true if the values in all fields are valid.

Usage

BinaryFingerprint$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

BinaryFingerprint$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

BinaryFingerprint$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

BinaryFingerprint$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `BinaryFingerprint$toList`
## ------------------------------------------------

# convert array of BinaryFingerprint (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

BioTransformerParameters Class

BioTransformerParameters Class

Format

An R6Class generator object

Details

Create a new BioTransformerParameters

Public fields

Methods

Public methods

• BioTransformerParameters$new()

• BioTransformerParameters$toJSON()

• BioTransformerParameters$toList()

• BioTransformerParameters$toSimpleType()

• BioTransformerParameters$fromJSON()

• BioTransformerParameters$toJSONString()

• BioTransformerParameters$fromJSONString()

• BioTransformerParameters$validateJSON()

• BioTransformerParameters$toString()

• BioTransformerParameters$isValid()

• BioTransformerParameters$getInvalidFields()

• BioTransformerParameters$print()

• BioTransformerParameters$clone()

Method new()

Initialize a new BioTransformerParameters class.

Usage

BioTransformerParameters$new(
  cyp450Mode,
  p2Mode,
  bioTransformerSequenceSteps,
  useDB = TRUE,
  ...
)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

BioTransformerParameters$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

BioTransformerParameters$toList()

Returns

BioTransformerParameters as a base R list.

Examples

# convert array of BioTransformerParameters (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert BioTransformerParameters to a base R type

Usage

BioTransformerParameters$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of BioTransformerParameters

Usage

BioTransformerParameters$fromJSON(input_json)

Arguments

Returns

the instance of BioTransformerParameters

Method toJSONString()

To JSON String

Usage

BioTransformerParameters$toJSONString(...)

Arguments

Returns

BioTransformerParameters in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of BioTransformerParameters

Usage

BioTransformerParameters$fromJSONString(input_json)

Arguments

Returns

the instance of BioTransformerParameters

Method validateJSON()

Validate JSON input with respect to BioTransformerParameters and throw an exception if invalid

Usage

BioTransformerParameters$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

BioTransformerParameters$toString()

Returns

String representation of BioTransformerParameters

Method isValid()

Return true if the values in all fields are valid.

Usage

BioTransformerParameters$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

BioTransformerParameters$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

BioTransformerParameters$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

BioTransformerParameters$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `BioTransformerParameters$toList`
## ------------------------------------------------

# convert array of BioTransformerParameters (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

BioTransformerSequenceStep Class

BioTransformerSequenceStep Class

Format

An R6Class generator object

Details

Create a new BioTransformerSequenceStep

Public fields

Methods

Public methods

• BioTransformerSequenceStep$new()

• BioTransformerSequenceStep$toJSON()

• BioTransformerSequenceStep$toList()

• BioTransformerSequenceStep$toSimpleType()

• BioTransformerSequenceStep$fromJSON()

• BioTransformerSequenceStep$toJSONString()

• BioTransformerSequenceStep$fromJSONString()

• BioTransformerSequenceStep$validateJSON()

• BioTransformerSequenceStep$toString()

• BioTransformerSequenceStep$isValid()

• BioTransformerSequenceStep$getInvalidFields()

• BioTransformerSequenceStep$print()

• BioTransformerSequenceStep$clone()

Method new()

Initialize a new BioTransformerSequenceStep class.

Usage

BioTransformerSequenceStep$new(
  metabolicTransformation = NULL,
  iterations = NULL,
  ...
)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

BioTransformerSequenceStep$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

BioTransformerSequenceStep$toList()

Returns

BioTransformerSequenceStep as a base R list.

Examples

# convert array of BioTransformerSequenceStep (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert BioTransformerSequenceStep to a base R type

Usage

BioTransformerSequenceStep$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of BioTransformerSequenceStep

Usage

BioTransformerSequenceStep$fromJSON(input_json)

Arguments

Returns

the instance of BioTransformerSequenceStep

Method toJSONString()

To JSON String

Usage

BioTransformerSequenceStep$toJSONString(...)

Arguments

Returns

BioTransformerSequenceStep in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of BioTransformerSequenceStep

Usage

BioTransformerSequenceStep$fromJSONString(input_json)

Arguments

Returns

the instance of BioTransformerSequenceStep

Method validateJSON()

Validate JSON input with respect to BioTransformerSequenceStep and throw an exception if invalid

Usage

BioTransformerSequenceStep$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

BioTransformerSequenceStep$toString()

Returns

String representation of BioTransformerSequenceStep

Method isValid()

Return true if the values in all fields are valid.

Usage

BioTransformerSequenceStep$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

BioTransformerSequenceStep$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

BioTransformerSequenceStep$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

BioTransformerSequenceStep$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `BioTransformerSequenceStep$toList`
## ------------------------------------------------

# convert array of BioTransformerSequenceStep (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

User/developer friendly parameter subset for the CANOPUS tool CANOPUS is parameter-free, so this object is just a flag that CANOPUS should be executed. Needs results from the FingerprintPrediction tool.

Canopus Class

Format

An R6Class generator object

Details

Create a new Canopus

Public fields

Methods

Public methods

• Canopus$new()

• Canopus$toJSON()

• Canopus$toList()

• Canopus$toSimpleType()

• Canopus$fromJSON()

• Canopus$toJSONString()

• Canopus$fromJSONString()

• Canopus$validateJSON()

• Canopus$toString()

• Canopus$isValid()

• Canopus$getInvalidFields()

• Canopus$print()

• Canopus$clone()

Method new()

Initialize a new Canopus class.

Usage

Canopus$new(enabled = NULL, ...)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

Canopus$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

Canopus$toList()

Returns

Canopus as a base R list.

Examples

# convert array of Canopus (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert Canopus to a base R type

Usage

Canopus$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of Canopus

Usage

Canopus$fromJSON(input_json)

Arguments

Returns

the instance of Canopus

Method toJSONString()

To JSON String

Usage

Canopus$toJSONString(...)

Arguments

Returns

Canopus in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of Canopus

Usage

Canopus$fromJSONString(input_json)

Arguments

Returns

the instance of Canopus

Method validateJSON()

Validate JSON input with respect to Canopus and throw an exception if invalid

Usage

Canopus$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

Canopus$toString()

Returns

String representation of Canopus

Method isValid()

Return true if the values in all fields are valid.

Usage

Canopus$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

Canopus$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

Canopus$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

Canopus$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `Canopus$toList`
## ------------------------------------------------

# convert array of Canopus (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

Container class that holds the CANOPUS compound class predictions for all predictable compound classes. This is the full CANOPUS result.

CanopusPrediction Class

Format

An R6Class generator object

Details

Create a new CanopusPrediction

Public fields

Methods

Public methods

• CanopusPrediction$new()

• CanopusPrediction$toJSON()

• CanopusPrediction$toList()

• CanopusPrediction$toSimpleType()

• CanopusPrediction$fromJSON()

• CanopusPrediction$toJSONString()

• CanopusPrediction$fromJSONString()

• CanopusPrediction$validateJSON()

• CanopusPrediction$toString()

• CanopusPrediction$isValid()

• CanopusPrediction$getInvalidFields()

• CanopusPrediction$print()

• CanopusPrediction$clone()

Method new()

Initialize a new CanopusPrediction class.

Usage

CanopusPrediction$new(classyFireClasses = NULL, npcClasses = NULL, ...)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

CanopusPrediction$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

CanopusPrediction$toList()

Returns

CanopusPrediction as a base R list.

Examples

# convert array of CanopusPrediction (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert CanopusPrediction to a base R type

Usage

CanopusPrediction$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of CanopusPrediction

Usage

CanopusPrediction$fromJSON(input_json)

Arguments

Returns

the instance of CanopusPrediction

Method toJSONString()

To JSON String

Usage

CanopusPrediction$toJSONString(...)

Arguments

Returns

CanopusPrediction in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of CanopusPrediction

Usage

CanopusPrediction$fromJSONString(input_json)

Arguments

Returns

the instance of CanopusPrediction

Method validateJSON()

Validate JSON input with respect to CanopusPrediction and throw an exception if invalid

Usage

CanopusPrediction$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

CanopusPrediction$toString()

Returns

String representation of CanopusPrediction

Method isValid()

Return true if the values in all fields are valid.

Usage

CanopusPrediction$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

CanopusPrediction$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

CanopusPrediction$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

CanopusPrediction$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `CanopusPrediction$toList`
## ------------------------------------------------

# convert array of CanopusPrediction (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

Compound Class

Compound Class

Format

An R6Class generator object

Details

Create a new Compound

Public fields

Methods

Public methods

• Compound$new()

• Compound$toJSON()

• Compound$toList()

• Compound$toSimpleType()

• Compound$fromJSON()

• Compound$toJSONString()

• Compound$fromJSONString()

• Compound$validateJSON()

• Compound$toString()

• Compound$isValid()

• Compound$getInvalidFields()

• Compound$print()

• Compound$clone()

Method new()

Initialize a new Compound class.

Usage

Compound$new(
  compoundId = NULL,
  name = NULL,
  rtStartSeconds = NULL,
  rtEndSeconds = NULL,
  neutralMass = NULL,
  features = NULL,
  consensusAnnotations = NULL,
  consensusAnnotationsDeNovo = NULL,
  customAnnotations = NULL,
  tags = NULL,
  ...
)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

Compound$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

Compound$toList()

Returns

Compound as a base R list.

Examples

# convert array of Compound (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert Compound to a base R type

Usage

Compound$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of Compound

Usage

Compound$fromJSON(input_json)

Arguments

Returns

the instance of Compound

Method toJSONString()

To JSON String

Usage

Compound$toJSONString(...)

Arguments

Returns

Compound in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of Compound

Usage

Compound$fromJSONString(input_json)

Arguments

Returns

the instance of Compound

Method validateJSON()

Validate JSON input with respect to Compound and throw an exception if invalid

Usage

Compound$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

Compound$toString()

Returns

String representation of Compound

Method isValid()

Return true if the values in all fields are valid.

Usage

Compound$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

Compound$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

Compound$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

Compound$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `Compound$toList`
## ------------------------------------------------

# convert array of Compound (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

Predicted compound class with name, probability and id if available. (ClassyFire and NPC). This can be seen as the set of classes a feature most likely belongs to

CompoundClass Class

Format

An R6Class generator object

Details

Create a new CompoundClass

Public fields

Methods

Public methods

• CompoundClass$new()

• CompoundClass$toJSON()

• CompoundClass$toList()

• CompoundClass$toSimpleType()

• CompoundClass$fromJSON()

• CompoundClass$toJSONString()

• CompoundClass$fromJSONString()

• CompoundClass$validateJSON()

• CompoundClass$toString()

• CompoundClass$isValid()

• CompoundClass$getInvalidFields()

• CompoundClass$print()

• CompoundClass$clone()

Method new()

Initialize a new CompoundClass class.

Usage

CompoundClass$new(
  type = NULL,
  level = NULL,
  levelIndex = NULL,
  name = NULL,
  description = NULL,
  id = NULL,
  probability = NULL,
  index = NULL,
  parentId = NULL,
  parentName = NULL,
  ...
)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

CompoundClass$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

CompoundClass$toList()

Returns

CompoundClass as a base R list.

Examples

# convert array of CompoundClass (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert CompoundClass to a base R type

Usage

CompoundClass$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of CompoundClass

Usage

CompoundClass$fromJSON(input_json)

Arguments

Returns

the instance of CompoundClass

Method toJSONString()

To JSON String

Usage

CompoundClass$toJSONString(...)

Arguments

Returns

CompoundClass in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of CompoundClass

Usage

CompoundClass$fromJSONString(input_json)

Arguments

Returns

the instance of CompoundClass

Method validateJSON()

Validate JSON input with respect to CompoundClass and throw an exception if invalid

Usage

CompoundClass$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

CompoundClass$toString()

Returns

String representation of CompoundClass

Method isValid()

Return true if the values in all fields are valid.

Usage

CompoundClass$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

CompoundClass$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

CompoundClass$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

CompoundClass$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `CompoundClass$toList`
## ------------------------------------------------

# convert array of CompoundClass (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

Container class that holds the most likely compound class for different levels of each ontology for a certain Compound/Feature/FormulaCandidate/PredictedFingerprint.

CompoundClasses Class

Format

An R6Class generator object

Details

Create a new CompoundClasses

Public fields

Methods

Public methods

• CompoundClasses$new()

• CompoundClasses$toJSON()

• CompoundClasses$toList()

• CompoundClasses$toSimpleType()

• CompoundClasses$fromJSON()

• CompoundClasses$toJSONString()

• CompoundClasses$fromJSONString()

• CompoundClasses$validateJSON()

• CompoundClasses$toString()

• CompoundClasses$isValid()

• CompoundClasses$getInvalidFields()

• CompoundClasses$print()

• CompoundClasses$clone()

Method new()

Initialize a new CompoundClasses class.

Usage

CompoundClasses$new(
  npcPathway = NULL,
  npcSuperclass = NULL,
  npcClass = NULL,
  classyFireLineage = NULL,
  classyFireAlternatives = NULL,
  ...
)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

CompoundClasses$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

CompoundClasses$toList()

Returns

CompoundClasses as a base R list.

Examples

# convert array of CompoundClasses (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert CompoundClasses to a base R type

Usage

CompoundClasses$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of CompoundClasses

Usage

CompoundClasses$fromJSON(input_json)

Arguments

Returns

the instance of CompoundClasses

Method toJSONString()

To JSON String

Usage

CompoundClasses$toJSONString(...)

Arguments

Returns

CompoundClasses in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of CompoundClasses

Usage

CompoundClasses$fromJSONString(input_json)

Arguments

Returns

the instance of CompoundClasses

Method validateJSON()

Validate JSON input with respect to CompoundClasses and throw an exception if invalid

Usage

CompoundClasses$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

CompoundClasses$toString()

Returns

String representation of CompoundClasses

Method isValid()

Return true if the values in all fields are valid.

Usage

CompoundClasses$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

CompoundClasses$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

CompoundClasses$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

CompoundClasses$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `CompoundClasses$toList`
## ------------------------------------------------

# convert array of CompoundClasses (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

CompoundImport Class

CompoundImport Class

Format

An R6Class generator object

Details

Create a new CompoundImport

Public fields

Methods

Public methods

• CompoundImport$new()

• CompoundImport$toJSON()

• CompoundImport$toList()

• CompoundImport$toSimpleType()

• CompoundImport$fromJSON()

• CompoundImport$toJSONString()

• CompoundImport$fromJSONString()

• CompoundImport$validateJSON()

• CompoundImport$toString()

• CompoundImport$isValid()

• CompoundImport$getInvalidFields()

• CompoundImport$print()

• CompoundImport$clone()

Method new()

Initialize a new CompoundImport class.

Usage

CompoundImport$new(features, name = NULL, ...)

Arguments

Method toJSON()

Convert to an R object. This method is deprecated. Use 'toSimpleType()' instead.

Usage

CompoundImport$toJSON()

Method toList()

Convert to a List

Convert the R6 object to a list to work more easily with other tooling.

Usage

CompoundImport$toList()

Returns

CompoundImport as a base R list.

Examples

# convert array of CompoundImport (x) to a data frame
\dontrun{
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df
}

Method toSimpleType()

Convert CompoundImport to a base R type

Usage

CompoundImport$toSimpleType()

Returns

A base R type, e.g. a list or numeric/character array.

Method fromJSON()

Deserialize JSON string into an instance of CompoundImport

Usage

CompoundImport$fromJSON(input_json)

Arguments

Returns

the instance of CompoundImport

Method toJSONString()

To JSON String

Usage

CompoundImport$toJSONString(...)

Arguments

Returns

CompoundImport in JSON format

Method fromJSONString()

Deserialize JSON string into an instance of CompoundImport

Usage

CompoundImport$fromJSONString(input_json)

Arguments

Returns

the instance of CompoundImport

Method validateJSON()

Validate JSON input with respect to CompoundImport and throw an exception if invalid

Usage

CompoundImport$validateJSON(input)

Arguments

Method toString()

To string (JSON format)

Usage

CompoundImport$toString()

Returns

String representation of CompoundImport

Method isValid()

Return true if the values in all fields are valid.

Usage

CompoundImport$isValid()

Returns

true if the values in all fields are valid.

Method getInvalidFields()

Return a list of invalid fields (if any).

Usage

CompoundImport$getInvalidFields()

Returns

A list of invalid fields (if any).

Method print()

Print the object

Usage

CompoundImport$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

CompoundImport$clone(deep = FALSE)

Arguments

Examples

## ------------------------------------------------
## Method `CompoundImport$toList`
## ------------------------------------------------

# convert array of CompoundImport (x) to a data frame
## Not run: 
library(purrr)
library(tibble)
df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
df

## End(Not run)

Description

CompoundsApi

Format

An R6Class generator object

Details

SIRIUS Nightsky API

REST API that provides the full functionality of SIRIUS and its web services as background service. It is intended as entry-point for scripting languages and software integration SDKs.This API is exposed by SIRIUS 6

The version of the OpenAPI document: 3.2 Generated by: https://openapi-generator.tech

Public fields

Methods

Public methods

• CompoundsApi$new()

• CompoundsApi$AddCompounds()

• CompoundsApi$AddCompoundsWithHttpInfo()

• CompoundsApi$DeleteCompound()

• CompoundsApi$DeleteCompoundWithHttpInfo()

• CompoundsApi$GetCompound()

• CompoundsApi$GetCompoundWithHttpInfo()

• CompoundsApi$GetCompoundQuantTable()

• CompoundsApi$GetCompoundQuantTableWithHttpInfo()

• CompoundsApi$GetCompounds()

• CompoundsApi$GetCompoundsWithHttpInfo()

• CompoundsApi$GetCompoundsPage()

• CompoundsApi$GetCompoundsPageWithHttpInfo()

• CompoundsApi$GetCompoundsSearchableFields()

• CompoundsApi$GetCompoundsSearchableFieldsWithHttpInfo()

• CompoundsApi$clone()

Method new()

Initialize a new CompoundsApi.

Usage

CompoundsApi$new(api_client)

Arguments

Method AddCompounds()

Import compounds and their contained features.

Usage

CompoundsApi$AddCompounds(
  project_id,
  compound_import,
  profile = NULL,
  opt_fields = list("none"),
  opt_fields_features = list("none"),
  data_file = NULL,
  ...
)

Arguments

Returns

array[Compound]

Method AddCompoundsWithHttpInfo()

Import compounds and their contained features.

Usage

CompoundsApi$AddCompoundsWithHttpInfo(
  project_id,
  compound_import,
  profile = NULL,
  opt_fields = list("none"),
  opt_fields_features = list("none"),
  data_file = NULL,
  ...
)

Arguments

Returns

API response (array[Compound]) with additional information such as HTTP status code, headers

Method DeleteCompound()

Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space.

Usage

CompoundsApi$DeleteCompound(project_id, compound_id, ...)

Arguments

Returns

void

Method DeleteCompoundWithHttpInfo()

Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space.

Usage

CompoundsApi$DeleteCompoundWithHttpInfo(project_id, compound_id, ...)

Arguments

Returns

API response (void) with additional information such as HTTP status code, headers

Method GetCompound()

Get compound (group of ion identities) with the given identifier from the specified project-space.

Usage

CompoundsApi$GetCompound(
  project_id,
  compound_id,
  ms_data_search_prepared = FALSE,
  opt_fields = list("none"),
  opt_fields_features = list("none"),
  data_file = NULL,
  ...
)

Arguments

Returns

Compound

Method GetCompoundWithHttpInfo()

Get compound (group of ion identities) with the given identifier from the specified project-space.

Usage

CompoundsApi$GetCompoundWithHttpInfo(
  project_id,
  compound_id,
  ms_data_search_prepared = FALSE,
  opt_fields = list("none"),
  opt_fields_features = list("none"),
  data_file = NULL,
  ...
)

Arguments

Returns

API response (Compound) with additional information such as HTTP status code, headers

Method GetCompoundQuantTable()

Returns the full quantification table of compounds

Usage

CompoundsApi$GetCompoundQuantTable(
  project_id,
  search_query = NULL,
  type = "APEX_INTENSITY",
  opt_fields = list("none"),
  data_file = NULL,
  ...
)

Arguments

Returns

QuantTable

Method GetCompoundQuantTableWithHttpInfo()

Returns the full quantification table of compounds

Usage

CompoundsApi$GetCompoundQuantTableWithHttpInfo(
  project_id,
  search_query = NULL,
  type = "APEX_INTENSITY",
  opt_fields = list("none"),
  data_file = NULL,
  ...
)

Arguments

Returns

API response (QuantTable) with additional information such as HTTP status code, headers

Method GetCompounds()

[DEPRECATED] List of all available compounds (group of ion identities) in the given project-space

Usage

CompoundsApi$GetCompounds(
  project_id,
  ms_data_search_prepared = FALSE,
  opt_fields = list("none"),
  opt_fields_features = list("none"),
  data_file = NULL,
  ...
)

Arguments

Returns

array[Compound]

Method GetCompoundsWithHttpInfo()

[DEPRECATED] List of all available compounds (group of ion identities) in the given project-space

Usage

CompoundsApi$GetCompoundsWithHttpInfo(
  project_id,
  ms_data_search_prepared = FALSE,
  opt_fields = list("none"),
  opt_fields_features = list("none"),
  data_file = NULL,
  ...
)

Arguments

Returns

API response (array[Compound]) with additional information such as HTTP status code, headers

Method GetCompoundsPage()

Page of available compounds (group of ion identities) in the given project-space

Usage

CompoundsApi$GetCompoundsPage(
  project_id,
  search_query = NULL,
  page = 0,
  size = 20,
  sort = NULL,
  ms_data_search_prepared = FALSE,
  opt_fields = list("none"),
  opt_fields_features = list("none"),
  data_file = NULL,
  ...
)

Arguments

Returns

PagedModelCompound

Method GetCompoundsPageWithHttpInfo()

Page of available compounds (group of ion identities) in the given project-space

Usage

CompoundsApi$GetCompoundsPageWithHttpInfo(
  project_id,
  search_query = NULL,
  page = 0,
  size = 20,
  sort = NULL,
  ms_data_search_prepared = FALSE,
  opt_fields = list("none"),
  opt_fields_features = list("none"),
  data_file = NULL,
  ...
)

Arguments

Returns

API response (PagedModelCompound) with additional information such as HTTP status code, headers

Method GetCompoundsSearchableFields()

Get all fields that can be used in the searchQuery parameter of compound endpoints

Usage

CompoundsApi$GetCompoundsSearchableFields(project_id, data_file = NULL, ...)

Arguments

Returns

array[SearchableField]

Method GetCompoundsSearchableFieldsWithHttpInfo()

Get all fields that can be used in the searchQuery parameter of compound endpoints

Usage

CompoundsApi$GetCompoundsSearchableFieldsWithHttpInfo(
  project_id,
  data_file = NULL,
  ...
)

Arguments

Returns

API response (array[SearchableField]) with additional information such as HTTP status code, headers

Method clone()

The objects of this class are cloneable with this method.

Usage

CompoundsApi$clone(deep = FALSE)

Arguments

Examples

## Not run: 
####################  AddCompounds  ####################

library(RSirius)
var_project_id <- "project_id_example" # character | project-space to import into.
var_compound_import <- c(CompoundImport$new(c(FeatureImport$new(123, 123, "name_example", "externalFeatureId_example", c("detectedAdducts_example"), 123, 123, 123, "NOT_APPLICABLE", BasicSpectrum$new("cosineQuery_example", c(SimplePeak$new(123, 123)), "name_example", 123, "collisionEnergy_example", "instrument_example", 123, 123, SimplePeak$new(123, 123), 123, 123, 123, 123, 123), c(BasicSpectrum$new("cosineQuery_example", c(SimplePeak$new(..., ...)), "name_example", 123, "collisionEnergy_example", "instrument_example", 123, 123, SimplePeak$new(123, 123), 123, 123, 123, 123, 123)), c(BasicSpectrum$new("cosineQuery_example", c(SimplePeak$new(..., ...)), "name_example", 123, "collisionEnergy_example", "instrument_example", 123, 123, SimplePeak$new(123, 123), 123, 123, 123, 123, 123)))), "name_example")) # array[CompoundImport] | the compound data to be imported
var_profile <- "profile_example" # character | profile describing the instrument used to measure the data. Used to merge spectra. (Optional)
var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' to override defaults. (Optional)
var_opt_fields_features <- c("none") # array[character] | set of optional fields of the nested features to be included. Use 'none' to override defaults. (Optional)

#Import compounds and their contained features.
api_instance <- rsirius_api$new()

# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$AddCompounds(var_project_id, var_compound_import, profile = var_profile, opt_fields = var_opt_fields, opt_fields_features = var_opt_fields_featuresdata_file = "result.txt")
result <- api_instance$compounds_api$AddCompounds(var_project_id, var_compound_import, profile = var_profile, opt_fields = var_opt_fields, opt_fields_features = var_opt_fields_features)
dput(result)


####################  DeleteCompound  ####################

library(RSirius)
var_project_id <- "project_id_example" # character | project-space to delete from.
var_compound_id <- "compound_id_example" # character | identifier of the compound to delete.

#Delete compound (group of ion identities) with the given identifier (and the included features) from the  specified project-space.
api_instance <- rsirius_api$new()

api_instance$compounds_api$DeleteCompound(var_project_id, var_compound_id)


####################  GetCompound  ####################

library(RSirius)
var_project_id <- "project_id_example" # character | project-space to read from.
var_compound_id <- "compound_id_example" # character | identifier of the compound (group of ion identities) to access.
var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast                             Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch                             peak assignments and reference spectra. (Optional)
var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional)
var_opt_fields_features <- c("none") # array[character] |  (Optional)

#Get compound (group of ion identities) with the given identifier from the specified project-space.
api_instance <- rsirius_api$new()

# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetCompound(var_project_id, var_compound_id, ms_data_search_prepared = var_ms_data_search_prepared, opt_fields = var_opt_fields, opt_fields_features = var_opt_fields_featuresdata_file = "result.txt")
result <- api_instance$compounds_api$GetCompound(var_project_id, var_compound_id, ms_data_search_prepared = var_ms_data_search_prepared, opt_fields = var_opt_fields, opt_fields_features = var_opt_fields_features)
dput(result)


####################  GetCompoundQuantTable  ####################

library(RSirius)
var_project_id <- "project_id_example" # character | project-space to read from.
var_search_query <- "search_query_example" # character | Optional query in lucene syntax selecting compounds by id. Omit this parameter to quantify all compounds. (Optional)
var_type <- "APEX_INTENSITY" # character | quantification type. (Optional)
var_opt_fields <- c(QuantTableOptField$new()) # array[QuantTableOptField] |  (Optional)

#Returns the full quantification table of compounds
api_instance <- rsirius_api$new()

# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetCompoundQuantTable(var_project_id, search_query = var_search_query, type = var_type, opt_fields = var_opt_fieldsdata_file = "result.txt")
result <- api_instance$compounds_api$GetCompoundQuantTable(var_project_id, search_query = var_search_query, type = var_type, opt_fields = var_opt_fields)
dput(result)


####################  GetCompounds  ####################

library(RSirius)
var_project_id <- "project_id_example" # character | project-space to read from.
var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast                             Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch                             peak assignments and reference spectra. (Optional)
var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional)
var_opt_fields_features <- c("none") # array[character] |  (Optional)

#[DEPRECATED] List of all available compounds (group of ion identities) in the given project-space
api_instance <- rsirius_api$new()

# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetCompounds(var_project_id, ms_data_search_prepared = var_ms_data_search_prepared, opt_fields = var_opt_fields, opt_fields_features = var_opt_fields_featuresdata_file = "result.txt")
result <- api_instance$compounds_api$GetCompounds(var_project_id, ms_data_search_prepared = var_ms_data_search_prepared, opt_fields = var_opt_fields, opt_fields_features = var_opt_fields_features)
dput(result)


####################  GetCompoundsPage  ####################

library(RSirius)
var_project_id <- "project_id_example" # character | project-space to read from.
var_search_query <- "search_query_example" # character | Optional search query in lucene syntax. Not yet supported for compounds; a non-empty                      query responds with 405 METHOD_NOT_ALLOWED. Omit this parameter to page over all compounds. (Optional)
var_page <- 0 # integer | Zero-based page index (0..N) (Optional)
var_size <- 20 # integer | The size of the page to be returned (Optional)
var_sort <- c("inner_example") # array[character] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (Optional)
var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast                             Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch                             peak assignments and reference spectra. (Optional)
var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional)
var_opt_fields_features <- c("none") # array[character] |  (Optional)

#Page of available compounds (group of ion identities) in the given project-space
api_instance <- rsirius_api$new()

# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetCompoundsPage(var_project_id, search_query = var_search_query, page = var_page, size = var_size, sort = var_sort, ms_data_search_prepared = var_ms_data_search_prepared, opt_fields = var_opt_fields, opt_fields_features = var_opt_fields_featuresdata_file = "result.txt")
result <- api_instance$compounds_api$GetCompoundsPage(var_project_id, search_query = var_search_query, page = var_page, size = var_size, sort = var_sort, ms_data_search_prepared = var_ms_data_search_prepared, opt_fields = var_opt_fields, opt_fields_features = var_opt_fields_features)
dput(result)


####################  GetCompoundsSearchableFields  ####################

library(RSirius)
var_project_id <- "project_id_example" # character | project space to read the searchable compound fields from.

#Get all fields that can be used in the searchQuery parameter of compound endpoints
api_instance <- rsirius_api$new()

# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetCompoundsSearchableFields(var_project_iddata_file = "result.txt")
result <- api_instance$compounds_api$GetCompoundsSearchableFields(var_project_id)
dput(result)



## End(Not run)

Description

Specifies which tools have been executed for the feature. Can be used to estimate which results can be expected. Null if it was not requested and non-null otherwise.

ComputedSubtools Class

Format

An R6Class generator object

Details

Create a new ComputedSubtools

Public fields

Methods

Public methods

• ComputedSubtools$new()

• ComputedSubtools$toJSON()

• ComputedSubtools$toList()

• ComputedSubtools$toSimpleType()

• ComputedSubtools$fromJSON()

• ComputedSubtools$toJSONString()

• ComputedSubtools$fromJSONString()

• ComputedSubtools$validateJSON()

• ComputedSubtools$toString()

• ComputedSubtools$isValid()

• ComputedSubtools$getInvalidFields()

• ComputedSubtools$print()

• ComputedSubtools$clone()