R: Get available genetic data profiles for a specific cancer...

cgdsr-getGeneticProfiles {cgdsr} | R Documentation

## Get available genetic data profiles for a specific cancer study

### Description

Queries the CGDS API and returns the available genetic profiles, e.g. mutation or copy number profiles, stored about a specific cancer study.

### Usage

    ## S3 method for class 'CGDS'
    getGeneticProfiles(x,cancerStudy,...)

### Arguments

`x` | A CGDS object (required)
`cancerStudy` | cancer study ID (required)
`...` | Not used.

### Value

A data.frame with six columns:

1. genetic_profile_id: a unique ID used to identify the genetic profile ID in subsequent interface calls. This is a human readable ID. For example, "gbm_tcga_mutations" identifies the TCGA GBM mutation genetic profile.

2. genetic_profile_name: short profile name.

3. genetic_profile_description: short profile description.

4. cancer_study_id: cancer study ID tied to this genetic profile. Will match the input cancer_study_id.

5. genetic_alteration_type: indicates the profile type. Will be one of: MUTATION, MUTATION_EXTENDED, COPY_NUMBER_ALTERATION, MRNA_EXPRESSION.

6. show_profile_in_analysis_tab: a boolean flag used for internal purposes (you can safely ignore it).

### Author(s)

<jacobsen@cbio.mskcc.org>

### References

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

### See Also

`cgdsr`,`CGDS`,`getCancerStudies`,`getCaseLists`,`getProfileData`

### Examples

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

    # Get list of cancer studys 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)

[Package cgdsr version 1.2.10 Index]