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

Description

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

Usage

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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

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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)

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