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

In kmezhoud/canceR: A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC

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/canceR documentation built on March 4, 2024, 12:34 a.m.