R: Retrieves genomic profile data for genes and genetic...

cgdsr-getProfileData {cgdsr} | R Documentation

## Retrieves genomic profile data for genes and genetic profiles.

### Description

Queries the CGDS API and returns data based on gene(s), genetic profile(s), and a case list.

### Usage

    ## S3 method for class 'CGDS'
    getProfileData(x,genes,geneticProfiles,caseList,cases,caseIdsKey,...)

### Arguments

`x` | A CGDS object (required)
`genes` | A vector of gene names or a String specifying a single gene (required)
`geneticProfiles` | A vector of genetic profile IDs or String specifying a single genetic profile (required)
`caseList` | A case list ID
`cases` | A vector of case IDs)
`caseIdsKey` | Only used by web portal.
`...` | Not used.

### Details

Only one list is allowed, specify either a list of genes or genetic profiles. The format of the output data.frame depends on if a single or a list of genes was specified in the arguments.

### Value

When requesting one or multiple genes and a single genetic profile, the function returns a data.frame with genetic profile data in columns for each gene.

When requesting a single gene and multiple genetic profiles, the function returns a data.frame containing columns with data for each genetic profile.

Cases can be specified either through a case list ID, or a vector of case IDs.

### Author(s)

<jacobsen@cbio.mskcc.org>

### References

cBio Cancer Genomics Portal: http://www.cbioportal.org/

### See Also

`cgdsr`,`CGDS`,`getCancerStudies`,`getGeneticProfiles`,`getCaseLists`

### Examples

    # Create CGDS object
    mycgds = CGDS("http://www.cbioportal.org/")

    # Get list of cancer studies at server
    getCancerStudies(mycgds)

    # Get available case lists (collection of samples) for a given cancer study
    mycancerstudy = getCancerStudies(mycgds)[2,1]
    mycaselist = getCaseLists(mycgds,mycancerstudy)[1,1]

    # Get available genetic profiles
    mygeneticprofile = getGeneticProfiles(mycgds,mycancerstudy)[1,1]

    # Get data slices for a specified list of genes, genetic profile and case list
    getProfileData(mycgds,c('BRCA1','BRCA2'),mygeneticprofile,mycaselist)

    # Get data slice for a single gene
    getProfileData(mycgds,'HMGA2',mygeneticprofile,mycaselist)

    # Get data slice for multiple genetic profiles and single gene
    getProfileData(mycgds,'HMGA2',getGeneticProfiles(mycgds,mycancerstudy)[c(1,2),1],mycaselist)

    # Get the same dataset from a vector of case IDs
    cases = unlist(strsplit(getCaseLists(mycgds,mycancerstudy)[1,'case_ids'],' '))
    getProfileData(mycgds,'HMGA2',getGeneticProfiles(mycgds,mycancerstudy)[c(1,2),1],cases=cases)

[Package cgdsr version 1.2.10 Index]