R/getTissues.R

In maddydoak/DoakThesis2020: Find Conserved Sex-Biased Genes Across Species

#' @export

# finds tissues that have have samples for all species and returns them in a list

getTissues <- function(metadata) {
  tissues <- list()
  
  # only adds tissues to the list for which EVERY species has samples
  for (tissue in unique(metadata$Tissue)) {
    nTotalCombinations = length(unique(metadata$Species))    # Number of species-sex combinations to check
    numCombinations = 0
    continue = TRUE
    while (continue) {
      for (species in unique(metadata$Species)) {
        if (tissue %in% metadata[which(metadata$Species == species), "Tissue"]) {
          numCombinations = numCombinations + 1
        }
      }
      continue = FALSE
    }
    if (numCombinations == nTotalCombinations) {
      tissues[[as.character(tissue)]] <- tissue
    }
  }
  
  return (tissues)
  
}