grepRef: search and get genetic profiles (CNA,mRNA, Methylation,...

In bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis

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)

bioCancer documentation built on Nov. 8, 2020, 6:26 p.m.