cgdsr-getGeneticProfiles: Get available genetic data profiles for a specific cancer...

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

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)

<[e-mail]>

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)

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