getMegaProfData {bioCancer} | R Documentation |
search and get genetic profiles (CNA,mRNA, Methylation, Mutation...) of gene list upper than 500
getMegaProfData(MegaGeneList, GenProf, Case, Class)
MegaGeneList |
A list of genes upper than 500 |
GenProf |
genetic profile reference |
Case |
Case reference |
Class |
indicates the panel ProfData or Mutdata |
See https://github.com/kmezhoud/bioCancer/wiki
A data frame with Genetic profile
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)