R: Get available case lists for a specific cancer study

cgdsr-getCaseLists {cgdsr} | R Documentation

## Get available case lists for a specific cancer study

### Description

Queries the CGDS API and returns available case lists for a specific cancer study.

### Usage

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

### Arguments

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

### Details

Queries the CGDS API and returns available case lists for a specific cancer study. For example, a within a particular study, only some cases may have sequence data, and another subset of cases may have been sequenced and treated with a specific therapeutic protocol. Multiple case lists may be associated with each cancer study, and this method enables you to retrieve meta-data regarding all of these case lists.

### Value

A data.frame with five columns:

1. case_list_id: a unique ID used to identify the case list ID in subsequent interface calls. This is a human readable ID. For example, "gbm_tcga_all" identifies all cases profiles in the TCGA GBM study.

2. case_list_name: short name for the case list.

3. case_list_description: short description of the case list.

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

5. case_ids: space delimited list of all case IDs that make up this case list.

### Author(s)

<jacobsen@cbio.mskcc.org>

### References

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

### See Also

`cgdsr`,`CGDS`,`getCancerStudies`,`getGeneticProfiles`,`getProfileData`

### 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)

[Package cgdsr version 1.2.10 Index]