getListProfData: get list of data frame with profiles data (CNA,mRNA,...

Description Usage Arguments Value Examples

View source: R/getListProfData.R

Description

get list of data frame with profiles data (CNA,mRNA, Methylation, Mutation...)

Usage

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getListProfData(panel, geneListLabel)

Arguments

panel

Panel name (string) in which Studies are selected. There are two panels ("Circomics" or "Networking")

geneListLabel

The label of GeneList. There are three cases: "Genes" user gene list, "Reactome_GeneList" GeneList plus genes from reactomeFI "file name" from Examples

Value

A LIST of profiles data (CNA, mRNA, Methylation, Mutation, miRNA, RPPA). Each dimension content a list of studies.

Examples

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cgds <- CGDS("http://www.cbioportal.org/public-portal/")
 ## Not run: 
geneList <- whichGeneList("73")
r_data <- new.env()
MutData <- cgdsr::getMutationData(cgds,"gbm_tcga_pub_all",
 "gbm_tcga_pub_mutations", geneList )
FreqMut <- getFreqMutData(list(ls1=MutData, ls2=MutData), "73")
input <- NULL
input[['StudiesIDCircos']] <- c("luad_tcga_pub","blca_tcga_pub")

ListProfData <- getListProfData(panel= "Circomics","73")

## End(Not run)

bioCancer documentation built on May 31, 2017, 3:33 p.m.