Namespace: tcga

tcga

Source:

Methods

(async, static) getMafInformationFromProjects(projects) → {Object}

Obtain MAF file ids and demograpic info of a list of projects
Parameters:
Name Type Description
projects array List with the projects of interest
Source:
Returns:
Object containing the list of maf files and samples demographic information
Type
Object
Example
let tcga = await import('https://raw.githubusercontent.com/YasCoMa/msig/main/mSigSDKScripts/tcga.js')
let projects = ['TCGA-LUSC', 'TCGA-OV']
var result = await tcga.getMafInformationFromProjects(projects)

(async, static) getProjectsByGene(genes) → {Object}

Obtain projects by gene
Parameters:
Name Type Description
genes array List with the genes of interest (ensemble id)
Source:
Returns:
Object containing the list of projects in which the genes are over/under expressed and the list of projects organized by genes
Type
Object
Example
let tcga = await import('https://raw.githubusercontent.com/YasCoMa/msig/main/mSigSDKScripts/tcga.js')
let genes = ['ENSG00000155657']
var result = await tcga.getProjectsByGene(genes)

(async, static) getTpmCountsByGenesFromFiles(genes, files) → {Object}

Obtain tpm count of a list of genes given sample file identifiers
Parameters:
Name Type Description
genes array List with the genes of interest (ensemble id)
files array List with the file ids
Source:
Returns:
Object containing the list of count ftpm and fpkm from each file organized by genes
Type
Object
Example
let tcga = await import('https://raw.githubusercontent.com/YasCoMa/msig/main/mSigSDKScripts/tcga.js')
let genes = ['ENSG00000155657']
let files = ['9e5f8edc-5074-43b7-a870-594aeb36e2aa', '8d5a94c8-b3d9-4991-8ce9-f7aa9189938c', 'dedf9f52-7ded-4cc5-bba2-da89a48b5176', '3aa53aa2-97cd-43a8-b7b1-09f0bf6381dd']
var result = await tcga.getTpmCountsByGenesFromFiles(genes, files)

(async, static) getTpmCountsByGenesOnProjects(genes, projects) → {Object}

Obtain tpm count of a list of genes in the sample files of the selected projects
Parameters:
Name Type Description
genes array List with the genes of interest (ensemble id)
projects array List with the projects of interest
Source:
Returns:
Object containing the list of count file ids and file descriptions organized by projects
Type
Object
Example
let genes = ['ENSG00000155657']
let projects = ['TCGA-LUSC', 'TCGA-OV']
var result = await tcga.getTpmCountsByGenesOnProjects(genes, projects)

(async, static) getVariantInformationFromMafFiles(res) → {Object}

Obtain mutations and variant information given MAF file identifiers
Parameters:
Name Type Description
res array Object containing the list of maf files and samples demographic information
Source:
Returns:
Object containing the list of patient mutation information
Type
Object
Example
let tcga = await import('https://raw.githubusercontent.com/YasCoMa/msig/main/mSigSDKScripts/tcga.js')
let res = { 'TCGA-LUSC': { 'maf_files': ['0b3d2db3-8ae3-4d39-bd9b-9d1e7a133b65', '9fed5902-6e95-4526-a119-ec4eade5576b' ] } }
var result = await tcga.getVariantInformationFromMafFiles(res)