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

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

Description

search and get genetic profiles (CNA,mRNA, Methylation, Mutation...) of gene list upper than 500

Usage

getMegaProfData(MegaGeneList, GenProf, Case, Class)

Arguments

MegaGeneList	A list of genes upper than 500
GenProf	genetic profile reference
Case	Case reference
Class	indicates the panel ProfData or Mutdata

Details

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

Value

A data frame with Genetic profile

Examples

GeneList <- c("ALK", "JAK3", "SHC3","TP53","MYC","PARP")
## Not run: 
cgds <- cgdsr::CGDS("http://www.cbioportal.org/")
listCase_gbm_tcga_pub <- cgdsr::getCaseLists(cgds,"gbm_tcga_pub")[,1]
listGenProf_gbm_tcga_pub <- cgdsr::getGeneticProfiles(cgds,"gbm_tcga_pub")[,1]

ProfData_Mut <- grepRef("gbm_tcga_pub_all", listCase_gbm_tcga_pub,
 "gbm_tcga_pub_mutations", listGenProf_gbm_tcga_pub, GeneList, Mut=1)

## End(Not run)

bioCancer documentation built on Nov. 8, 2020, 6:26 p.m.