data-raw/mutations.R

In shunsambongi/sambcdata: Select TCGA Breast Cancer datasets

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

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

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

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

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

mutations <- readr::read_tsv(destfile)

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

mutations <-
  mutations %>%
  dplyr::filter(!is.na(sample)) %>%
  dplyr::rename(gene = sample)

devtools::use_data(mutations, overwrite = TRUE)