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/public-portal/")
    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 1.8.0 Index]