data-raw/cnvs.R

In shunsambongi/sambcdata: Select TCGA Breast Cancer datasets

# DOWNLOAD DATA -----------------------------------

url <- "https://tcga.xenahubs.net/download/TCGA.BRCA.sampleMap/Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes.gz"

destfile <- "data-raw/cnvs.gz"

httr::GET(url, httr::write_disk(destfile, overwrite = TRUE))

# SAVE DATA -----------------------------------------

cnvs <- readr::read_tsv(destfile)

`%>%` <- magrittr::`%>%`

cnvs <-
  cnvs %>%
  dplyr::rename(gene = `Gene Symbol`)

devtools::use_data(cnvs)