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

In kmezhoud/bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis

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.