#' mRNA_exp
#'
#' Given some genes get mRNA expression for all samples in TCGA cohort
#'
#' @param genes Genes to make a subselection from (to large otherwise)
#'
#' @return mRNA_DF
#' @export
#' @examples
#' mRNA_exp(c("ACC","XX","YY"))
#' @import dplyr
#' @import data.table
mRNA_exp <- function(genes){
setwd(main_wd)
file_list <- list.files(pattern="_normalized__data.data.txt",recursive = TRUE)
print("reading mRNA files")
read_mRNASeq <- function(files){
Table1 <- fread(files,header=TRUE,stringsAsFactors = FALSE)
#Filter only for genes in function argument.
Table1$`Hybridization REF` <- gsub("\\|.*$","",Table1$`Hybridization REF`)
Table1 <- Table1 %>% filter(Table1$`Hybridization REF` %in% genes)
return(Table1)
}
#file_list <- file_list[1:3]
mRNA_DF <- do.call("cbind",lapply(file_list ,read_mRNASeq))
mRNA_DF <- mRNA_DF[, !duplicated(colnames(mRNA_DF))]
rownames(mRNA_DF) <- as.vector(mRNA_DF$`Hybridization REF`)
mRNA_DF<- mRNA_DF[, !colnames(mRNA_DF)=="Hybridization REF"]
colnames(mRNA_DF) <- gsub("-[A-Z0-9]*-[A-Z0-9]*-[A-Z0-9]*$","",colnames(mRNA_DF))
setwd(main_wd)
#write.table(dataset,"PANCAN_mRNA_expression.txt")
#save(dataset,file="DNArep_mRNA_exp.rda")
return(mRNA_DF)
}
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