getMegaProfData {bioCancer}R Documentation

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

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)

[Package bioCancer version 1.21.02 Index]