grepRef {bioCancer} | R Documentation

## search and get genetic profiles (CNA,mRNA, Methylation, Mutation...)

### Description

search and get genetic profiles (CNA,mRNA, Methylation, Mutation...)

### Usage

    grepRef(regex1, listRef1,regex2, listRef2, GeneList,Mut)

### Arguments

`regex1` | Case id (cancer_study_id_[mutations, cna, methylation, mrna ]).
`listRef1` | A list of cases for one study.
`regex2` | Genetic Profile id (cancer_study_id_[mutations, cna, methylation, mrna ]).
`listRef2` | 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

    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 1.22.0 Index]