grepRef {bioCancer} | R Documentation |
search and get genetic profiles (CNA,mRNA, Methylation, Mutation...)
grepRef(regex1, listRef1,regex2, listRef2, GeneList,Mut)
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) |
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)