# UMCCR Cancer Genes
require(here)
require(readr)
require(dplyr)
tmp <- tempfile()
download.file(
url = "https://raw.githubusercontent.com/umccr/genes/893a655801ce92715f05517b5052e4e81904e870/panels/umccr_2019-03-20.tsv",
destfile = tmp
)
readr::read_tsv(tmp) |>
dplyr::select(symbol, tumorsuppressor, oncogene) |>
readr::write_tsv(here("inst/extdata/ref/umccr_cancer_genes_2019-03-20.tsv"))
tmp2 <- tempfile()
download.file(
"https://raw.githubusercontent.com/umccr/workflows/8d06a16a0199ccf94b666f9ec027efce8af1110b/genes/cancer_genes/umccr_cancer_genes.hg38.coding.bed",
destfile = tmp2
)
readr::read_tsv(tmp2, col_names = c("chr", "start", "end", "symbol"), col_types = "ciic") |>
readr::write_tsv(here("inst/extdata/ref/umccr_cancer_genes_hg38_coding.bed"))
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