cgdsr-getCaseLists: Get available case lists for a specific cancer study

In cgdsr: R-Based API for Accessing the MSKCC Cancer Genomics Data Server (CGDS)

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)

<[e-mail]>

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)

cgdsr documentation built on June 27, 2019, 5:07 p.m.