R/purity_ploidy.R

In seandavi/TargetOsteoAnalysis: Access Open-access TARGET Osteosarcoma Data

#' Load Purity and Ploidy estimates
#'
#' Results from PureCN run on discovery and
#' validation sets.
#'
#' @import dplyr
#' @import magrittr
#' @importFrom readr read_tsv
#'
#' @return A \code{data.frame} with columns Source,
#'     Purity, Ploidy, and dataset
#'
#' @examples
#' pure = target_purity()
#' head(pure)
#' library(magrittr)
#' library(dplyr)
#' pure %>%
#'   group_by(dataset) %>%
#'   summarise(medploidy = median(Ploidy, na.rm=TRUE),
#'             medpurity = median(Purity, na.rm=TRUE),
#'             lowpurity = quantile(Purity, 0.1, na.rm=TRUE))
#' library(ggplot2)
#' p = ggplot(pure, aes(x=Purity)) +
#'   geom_density(aes(group=dataset, color=dataset)) +
#'   ggtitle('Tumor Purity Estimates')
#' print(p)
#' 
#' @export
target_purity <- function() {
  d_fname = file.path(system.file('extdata', package='TargetOsteoAnalysis'), "OS_dis_pureCN_all.txt.gz")
  dis = suppressMessages(read_tsv(d_fname, na = c('?'))) %>%
    select(Sampleid, Purity, Ploidy) %>%
    rename(Source = Sampleid) %>%
    mutate(Source = sub('_.*','', Source)) %>%
    mutate(dataset = "Discovery")
  v_fname = file.path(system.file('extdata', package='TargetOsteoAnalysis'), "OS_Val_Roche_Purecn.txt.gz")
  val = suppressMessages(read_tsv(v_fname, na = c('?'))) %>%
    select(Source, Purity, Ploidy) %>%
      mutate(dataset = "Validation")
  ret = bind_rows(dis, val)
  ret = ret[apply(ret,1,function(r) !any(is.na(r))),]
  return(ret)
}