data-raw/phenotypes.R

In shunsambongi/sambcdata: Select TCGA Breast Cancer datasets

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

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

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

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

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

phenotypes <- readr::read_tsv(destfile)

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

phenotypes <-
  phenotypes %>%
  dplyr::rename(sample = sampleID)

devtools::use_data(phenotypes)