inst/extdata/blca_cnaseq.R

In TCGAutils: TCGA utility functions for data management

## Generate blca_cnaseq data
if (!requireNamespace("RTCGAToolbox"))
    stop("Download package 'RTCGAToolbox' to regenerate data")

library(RTCGAToolbox)

blca <- getFirehoseData("BLCA", clinical = FALSE,
    CNASeq = TRUE, destdir = tempdir())
bl <- getData(blca, "CNASeq")

set.seed(777)
blsplit <- lapply(split(bl, bl[["Sample"]]), function(x)
    x[sample(seq_len(nrow(x)), 2L), ])

blframe <- dplyr::bind_rows(blsplit)
blca_cnaseq <- blframe[c(TRUE, TRUE, FALSE, FALSE), ]

write.table(blca_cnaseq, file = "inst/extdata/blca_cnaseq.txt")