JSDoc: Namespace: mSigPortalData

Source:

main.js, line 82

Methods

(static) extractMutationalSpectra(data, groupNameopt) → {Object}

Extracts the mutational spectra out of the mSigPortal API call.

Parameters:

Name	Type	Attributes	Default	Description
`data`	Array.<Object>			An array of objects containing the data from the mSigPortal API call.
`groupName`	string	<optional>	"sample"	The name of the group to extract the mutational spectra from.

Source:

main.js, line 757

Returns:

An object containing the mutational spectra data grouped by the specified group name.

Type: Object

(static) formatMutationalSpectraData(mutationalSpectrum, sample) → {Array.<Object>}

Converts the mutational spectra data to a format that can be used to create a Plotly chart.

Parameters:

Name	Type	Description
`mutationalSpectrum`	Object	An object containing the mutational spectra data.
`sample`	string	The name of the sample.

Source:

main.js, line 705

Returns:

The data in a format that can be used to create a Plotly chart. The data is an array of objects. Each object has a name, x, y, and type property. The name property is the name of the mutation type. The x property is an array of the mutation names. The y property is an array of the mutation frequencies. The type property is the type of substitution that takes place.

Type: Array.<Object>

(async, static) getMutationalSignatureActivityData(studyopt, genomeDataTypeopt, cancerTypeopt, signatureSetNameopt, numberOfResultsopt) → {Promise.<Object>}

Retrieves mutational signature landscape data from the mutational-signatures API.

Parameters:

Name	Type	Attributes	Default	Description
`study`	string	<optional>	"PCAWG"	The name of the study. Default value is "PCAWG".
`genomeDataType`	string	<optional>	"WGS"	The type of genome data. Default value is "WGS".
`cancerType`	string	<optional>	""	The name of the cancer type. Default value is an empty string.
`signatureSetName`	string	<optional>	"COSMIC_v3_Signatures_GRCh37_SBS96"	The name of the signature set. Default value is "COSMIC_v3_Signatures_GRCh37_SBS96".
`numberOfResults`	number	<optional>	10	The maximum number of results to be returned. Default value is 10.

Source:

mSigSDKScripts/mSigPortalAPIs.js, line 298

Returns:

- A Promise that resolves to the JSON data of the mutational signature landscape.

Type: Promise.<Object>

(async, static) getMutationalSignatureActivityOptions(studyopt, genomeDataTypeopt, numberOfResultsopt) → {Promise.<Array>}

Retrieves a list of mutational signature activity options from the mutational signatures API.

Parameters:

Name	Type	Attributes	Default	Description
`study`	string	<optional>	"PCAWG"	The name of the study to retrieve mutational signature activity options for. Defaults to "PCAWG".
`genomeDataType`	string	<optional>	"WGS"	The genome data type to retrieve mutational signature activity options for. Defaults to "WGS".
`numberOfResults`	number	<optional>	10	The number of results to retrieve. Defaults to 10.

Source:

mSigSDKScripts/mSigPortalAPIs.js, line 278

Returns:

- A promise that resolves with an array of mutational signature activity options.

Type: Promise.<Array>

(async, static) getMutationalSignatureAssociationData(studyopt, genomeDataTypeopt, cancerTypeopt, numberOfResultsopt) → {Promise.<object>}

Retrieves mutational signature association data from a specified cancer study using the provided parameters.

Parameters:

Name	Type	Attributes	Default	Description
`study`	string	<optional>	"PCAWG"	The name of the cancer study. Default is "PCAWG".
`genomeDataType`	string	<optional>	"WGS"	The type of genome data used. Default is "WGS".
`cancerType`	string	<optional>	"Biliary-AdenoCA"	The type of cancer. Default is "Biliary-AdenoCA".
`numberOfResults`	number	<optional>	10	The maximum number of results to return. Default is 10.

Source:

mSigSDKScripts/mSigPortalAPIs.js, line 250

Returns:

- A Promise that resolves to the JSON response containing the mutational signature association data.

Type: Promise.<object>

(async, static) getMutationalSignatureAssociationOptions(studyopt, genomeDataTypeopt, numberOfResultsopt) → {Promise.<Array>}

Fetches the mutational signature association options from the API endpoint

Parameters:

Name	Type	Attributes	Default	Description
`study`	string	<optional>	"PCAWG"	The name of the study. Defaults to "PCAWG".
`genomeDataType`	string	<optional>	"WGS"	The type of genome data. Defaults to "WGS".
`numberOfResults`	number	<optional>	10	The number of results to return. Defaults to 10.

Source:

mSigSDKScripts/mSigPortalAPIs.js, line 227

Throws:

- If an error occurs during the fetching or caching of the data.
Type Error

Returns:

- A Promise that resolves to an array of mutational signature association options.

Type: Promise.<Array>

(async, static) getMutationalSignatureEtiologyData(studyopt, genomeDataTypeopt, signatureNameopt, cancerTypeopt, numberOfResultsopt) → {Promise}

Retrieves mutational signature etiology data from the Cancer Genomics Research Laboratory (CGR) website.

Parameters:

Name	Type	Attributes	Default	Description
`study`	string	<optional>	"PCAWG"	The study name. Default is "PCAWG".
`genomeDataType`	string	<optional>	"WGS"	The genome data type. Default is "WGS".
`signatureName`	string	<optional>	"SBS3"	The signature name. Default is "SBS3".
`cancerType`	string	<optional>	""	The cancer type. Default is an empty string.
`numberOfResults`	number	<optional>	10	The number of results to return. Default is 10.

Source:

mSigSDKScripts/mSigPortalAPIs.js, line 414

Returns:

A promise that resolves to the mutational signature etiology data in JSON format.

Type: Promise

(async, static) getMutationalSignatureEtiologyOptions(studyopt, genomeDataTypeopt, signatureNameopt, cancerTypeopt, numberOfResultsopt) → {Promise.<Object>}

Retrieves the etiology options for a given mutational signature from the Cancer.gov Mutational Signatures API.

Parameters:

Name	Type	Attributes	Default	Description
`study`	string	<optional>	"PCAWG"	The name of the study to retrieve etiology options for. Defaults to "PCAWG".
`genomeDataType`	string	<optional>	"WGS"	The type of genome data to retrieve etiology options for. Defaults to "WGS".
`signatureName`	string	<optional>	"SBS3"	The name of the mutational signature to retrieve etiology options for. Defaults to "SBS3".
`cancerType`	string	<optional>	""	The cancer type to retrieve etiology options for. Defaults to an empty string.
`numberOfResults`	number	<optional>	10	The maximum number of results to return. Defaults to 10.

Source:

mSigSDKScripts/mSigPortalAPIs.js, line 364

Returns:

A promise that resolves to an object representing the etiology options for the specified mutational signature. The object will have the following properties: etiology: An array of strings representing the possible etiologies for the mutational signature. etiology_display: An array of strings representing the display names for the possible etiologies. signatureName: The name of the mutational signature. study: The name of the study. genome_data_type: The type of genome data. cancer_type: The cancer type.

Type: Promise.<Object>

(async, static) getMutationalSignatureLandscapeData(studyopt, genomeDataTypeopt, cancerTypeopt, signatureSetNameopt, numberOfResultsopt) → {Promise.<object>}

Retrieves mutational signature landscape data from an API endpoint.

Parameters:

Name	Type	Attributes	Default	Description
`study`	string	<optional>	"PCAWG"	The study to retrieve data from.
`genomeDataType`	string	<optional>	"WGS"	The type of genomic data used in the study.
`cancerType`	string	<optional>	""	The type of cancer to retrieve data for.
`signatureSetName`	string	<optional>	"COSMIC_v3_Signatures_GRCh37_SBS96"	The name of the mutational signature set to retrieve.
`numberOfResults`	number	<optional>	10	The number of results to retrieve.

Source:

mSigSDKScripts/mSigPortalAPIs.js, line 330

Returns:

- A promise that resolves to an object containing the mutational signature landscape data.

Type: Promise.<object>

(async, static) getMutationalSignaturesData(genomeDataTypeopt, signatureSetNameopt, mutationTypeopt, matrixopt, numberofResultsopt) → {Promise.<Object>}

Parameters:

Name	Type	Attributes	Default	Description
`genomeDataType`	string	<optional>	"WGS"	The type of genome data to use. Defaults to "WGS".
`signatureSetName`	string	<optional>	"COSMIC_v3_Signatures_GRCh37_SBS96"	The name of the signature set to use. Defaults to "COSMIC_v3_Signatures_GRCh37_SBS96".
`mutationType`	string	<optional>	"SBS"	The type of mutation to analyze. Defaults to "SBS".
`matrix`	number	<optional>	96	The size of the mutational signature matrix. Defaults to 96.
`numberofResults`	number	<optional>	10	The number of results to retrieve. Defaults to 10.

Source:

mSigSDKScripts/mSigPortalAPIs.js, line 30

Throws:

- If there was an issue fetching the mutational signatures data.
Type Error

Returns:

- A Promise that resolves to the unformatted mutational signatures data as JSON.

Type: Promise.<Object>

Example

const mutationalSignatures = await getMutationalSignaturesData("WGS", "COSMIC_v3_Signatures_GRCh37_SBS96", "SBS", 96, 10);
console.log(mutationalSignatures);

(async, static) getMutationalSignaturesOptions(genomeDataTypeopt, mutationTypeopt) → {Promise}

Retrieves the mutational signature options from the specified API endpoint.

Parameters:

Name	Type	Attributes	Default	Description
`genomeDataType`	string	<optional>	"WGS"	The genome data type to use. Defaults to "WGS".
`mutationType`	string	<optional>	"SBS"	The mutation type to use. Defaults to "SBS".

Source:

mSigSDKScripts/mSigPortalAPIs.js, line 5

Returns:

A Promise that resolves to the mutational signature options in JSON format.

Type: Promise

Example

const mutationalSignatures = await getMutationalSignaturesOptions("WGS", "SBS");
console.log(mutationalSignatures);

(async, static) getMutationalSignaturesSummary(numberofResultsopt, signatureSetNameopt) → {Promise.<Object>}

Returns a summary of mutational signatures based on the provided signature set name and number of results.

Parameters:

Name	Type	Attributes	Default	Description
`numberofResults`	number	<optional>	10	The number of results to retrieve. Defaults to 10 if not provided.
`signatureSetName`	string	<optional>	"COSMIC_v3.3_Signatures"	The name of the signature set to retrieve. Defaults to "COSMIC_v3.3_Signatures" if not provided.

Source:

mSigSDKScripts/mSigPortalAPIs.js, line 65

Throws:

- Throws an error if there was an issue fetching the mutational signature summary.
Type Error

Returns:

- A Promise that resolves to an object representing the mutational signature summary.

Type: Promise.<Object>

Example

const summary = await getMutationalSignaturesSummary(20, "COSMIC_v3.3_Signatures");
console.log(summary);

(async, static) getMutationalSpectrumData(studyopt, samplesopt, genomeDataTypeopt, cancerTypeopt, mutationTypeopt, matrixSizeopt) → {Promise}

Fetches mutational spectrum data from the Cancer Genomics Data Server API and returns it in a formatted way.

Parameters:

Name	Type	Attributes	Default	Description
`study`	string	<optional>	"PCAWG"	The study identifier.
`samples`	Array.<string> \| null	<optional>	null	The sample identifier(s) to query data for.
`genomeDataType`	string	<optional>	"WGS"	The genome data type identifier.
`cancerType`	string	<optional>	"Lung-AdenoCA"	The cancer type identifier.
`mutationType`	string	<optional>	"SBS"	The mutation type identifier.
`matrixSize`	number	<optional>	96	The size of the mutational spectrum matrix.

Source:

mSigSDKScripts/mSigPortalAPIs.js, line 116

Returns:

- A promise that resolves to the formatted mutational spectrum data.

Type: Promise

(async, static) getMutationalSpectrumOptions(studyopt, genomeDataTypeopt, cancerTypeopt, numberOfResultsopt) → {Promise.<Object>}

Retrieves mutational spectrum options from the mutational signatures API.

Parameters:

Name	Type	Attributes	Default	Description
`study`	string	<optional>	"PCAWG"	The name of the study to retrieve options for. Defaults to "PCAWG".
`genomeDataType`	string	<optional>	"WGS"	The genome data type to retrieve options for. Defaults to "WGS".
`cancerType`	string	<optional>	"Lung-AdenoCA"	The cancer type to retrieve options for. Defaults to "Lung-AdenoCA".
`numberOfResults`	number	<optional>	10	The number of results to retrieve. Defaults to 10.

Source:

mSigSDKScripts/mSigPortalAPIs.js, line 92

Returns:

A Promise that resolves to the JSON response from the mutational signatures API.

Type: Promise.<Object>

(async, static) getMutationalSpectrumSummary(studyopt, genomeDataTypeopt, cancerTypeopt, numberOfResultsopt) → {Promise}

Fetches the mutational spectrum summary from the mutational signatures API based on the given parameters.

Parameters:

Name	Type	Attributes	Default	Description
`study`	string	<optional>	"PCAWG"	The name of the cancer genome study. Default is "PCAWG".
`genomeDataType`	string	<optional>	"WGS"	The type of genomic data used. Default is "WGS".
`cancerType`	string	<optional>	"Lung-AdenoCA"	The type of cancer. Default is "Lung-AdenoCA".
`numberOfResults`	number	<optional>	10	The number of results to be returned. Default is 10.

Source:

mSigSDKScripts/mSigPortalAPIs.js, line 198

Throws:

- If the API request fails.
Type Error

Returns:

- A Promise that resolves to a JSON object representing the mutational spectrum summary.

Type: Promise