getProfData: search and get genetic profiles (CNA,mRNA, Methylation,...

View source: R/getListProfData.R

getProfDataR Documentation

search and get genetic profiles (CNA,mRNA, Methylation, Mutation...)

Description

search and get genetic profiles (CNA,mRNA, Methylation, Mutation...)

Usage

getProfData(study,genProf, listGenProf, GeneList, Mut)

Arguments

study

Study ID

genProf

Genetic Profile id (cancer_study_id_[mutations, cna, methylation, mrna ]).

listGenProf

A list of Genetic Profiles for one study.

GeneList

A list of genes

Mut

Condition to set if the genetic profile is mutation or not (0,1)

Details

See https://github.com/kmezhoud/bioCancer/wiki

Value

A data frame with Genetic profile

Examples

cgds <- cBioPortal(
hostname = "www.cbioportal.org",
protocol = "https",
api = "/api/v2/api-docs"
)
## Not run: 
getDataByGenes( api =  cgds,
studyId = "gbm_tcga_pub",
genes = c("NF1", "TP53", "ABL1"),
by = "hugoGeneSymbol",
molecularProfileIds = "gbm_tcga_pub_mrna"
)

## End(Not run)

kmezhoud/bioCancer documentation built on Feb. 17, 2024, 10:29 a.m.