R/get_tcga_copynumber_results.R

In CRI-iAtlas/iatlas-feather-files: iAtlas Data

get_tcga_copynumber_results <- function() {
  paths <- c("syn21781426", "syn21781395", "syn21781409") %>%
    purrr::map(synapser::synGet) %>%
    purrr::map(purrr::pluck, "path")

  purrr::walk(paths, load)
  for (path in paths) {
    load(path)
  }

  tbl <-
    list(immunetable, studytable, subtypetable) %>%
    dplyr::bind_rows() %>%
    dplyr::select(
      tag = Group,
      hgnc = Gene,
      feature = Metric,
      direction = Direction,
      mean_normal = Mean_Normal,
      mean_cnv = Mean_CNV,
      t_stat = T_stat,
      p_value = Pvalue,
      log10_p_value = Neg_log10_pvalue
    ) %>%
    dplyr::mutate(feature = stringr::str_replace_all(feature, "\\.", "_"))

  # Convert HGNC to Entrez ---------------------------------------------------
  tbl <- tbl %>% dplyr::inner_join(iatlas.data::get_tcga_gene_ids(), by = "hgnc")

  # Clean up the data ---------------------------------------------------
  tbl <- tbl %>% dplyr::distinct(entrez, feature, tag, direction, mean_normal, mean_cnv, p_value, log10_p_value, t_stat) %>%
    dplyr::arrange(entrez, feature, tag, direction)

  rm(immunetable)
  rm(studytable)
  rm(subtypetable)
  return(tbl)
}