R/makeOrthologTable.R

In maddydoak/Doak.Thesis.2020: Find Conserved Sex-Biased Genes Across Species

#' @export

makeOrthologTable <- function (old_orthologs, spec_orth, prefix) {
  library(tidyverse)
  source("R/addXenLaeOrthologs.R")
  
  new_column <- paste(prefix, ".gene.stable.ID", sep = "")
  
  # Adds new species' genes to ortholog table
  old_orthologs[new_column] <- as.character(c(NA))                                 # Adds newly created species label as a column
  
  if (prefix == "XenLae") {
    old_orthologs <- addXenLaeOrthologs(old_orthologs, spec_orth, new_column)      # Handles Xenopus laevis polyploidy problem
  }
  else {
    for (row in 1:nrow(old_orthologs)) {
      gene <- old_orthologs[row, "Gene.name"][[1]]
      gene_ref_ID <- NA
      if (length(which(spec_orth$Gene.name == gene |
                       spec_orth$Gene.name == tolower(gene) |
                       spec_orth$Gene.name == toupper(gene))) > 0) {
        gene_ref_ID <- as.character(spec_orth[which(spec_orth$Gene.name == gene |
                                                      spec_orth$Gene.name == tolower(gene) |
                                                      spec_orth$Gene.name == toupper(gene)), "Ref.ID"][[1]])
        old_orthologs[row, new_column] <- gene_ref_ID
      }
    }
  }
  all_orthologs <- old_orthologs[which(!is.na(old_orthologs[new_column])), ]      # Only keeps genes for which there is data for new species

  return(all_orthologs)
}