R/filtering_DE.R

In isabellagrassucci/autogo_cp: Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations

#' @title Filtering DESeq2 results
#'
#' @description We could be in a position to carry out multiple filters on the results of the differential analysis, in order not to repeat all the deseq_analysis.R code which provides for the actual computation of the differential analysis, the filtering_DE.R function has been implemented to be able to filter the file(s) " * _allres.tsv " and generate all the folders and files associated with the specific filters applied.
#' @description The function automatically searches inside the folders where_results and outfolder the file(s) (See ?deseq_analysis()) "_allres.tsv" and generates folders and files in the same folders with the new filters for foldchange and pvalue respectively.
#' @param padj_threshold (Default = 0.05) Threshold value for adjusted p-value filtering.
#' @param log2FC_threshold (Default = 0) Threshold value for log2(Fold Change) filtering.
#' @param where_results (Default = "./") Folder in which the new output is written.
#' @param outfolder (Default = "results/") Name of the folder in which the new output is written.
#' @param save_excel (Default = FALSE) Write output in MS Excel file format (.xlsx).
#' @export



filtering_DE <- function(padj_threshold=0.05, log2FC_threshold=0, where_results = "./", outfolder = "results/", save_excel = F) {
  all_res <- list.files(path = paste0(where_results,outfolder), pattern = "_allres.tsv", recursive = T)
  all_res <- paste0(where_results,outfolder,all_res)
  readed <- lapply(all_res, function (x) read_tsv(x, col_types = cols()))
  names(readed) <- gsub(paste0(where_results,outfolder,"|\\/.*"),"",all_res)

  for (files in names(readed)) {
    data <- readed[[files]]
    filtered <- data %>%
      filter(padj < padj_threshold & abs(log2FoldChange) > log2FC_threshold)

    groups_fold <- paste0(where_results,outfolder,files,"/filtered_DE_",files,"_thFC",log2FC_threshold,"_thPval",padj_threshold)
    groups_fold_thresh_up_down <- paste0(groups_fold,"/up_down_genes_",files,"_thFC",log2FC_threshold,"_thPval",padj_threshold)
    groups_fold_thresh_up <- paste0(groups_fold,"/up_genes_",files,"_thFC",log2FC_threshold,"_thPval",padj_threshold)
    groups_fold_thresh_down <- paste0(groups_fold,"/down_genes_",files,"_thFC",log2FC_threshold,"_thPval",padj_threshold)

    #saving filtered results in different folders by thresholds
    if(!dir.exists(groups_fold)) dir.create(groups_fold, recursive=T)
    write_tsv(filtered, paste0(groups_fold,"/filtered_DE_",files,"_thFC",log2FC_threshold,"_thPval",padj_threshold,".tsv"))
    if (save_excel) write.xlsx(filtered, file=paste0(groups_fold,"/filtered_DE_",files,"_thFC",log2FC_threshold,"_thPval",padj_threshold,".xlsx"),row.names = F)

    #saving gene lists
    if(!dir.exists(groups_fold_thresh_up_down)) dir.create(groups_fold_thresh_up_down, recursive=T)
    write.table(filtered$genes, paste0(groups_fold_thresh_up_down, "/up_down_genes_list_", files,"_thFC",log2FC_threshold,"_thPval",padj_threshold,".txt"), quote = F, row.names = F, col.names = F)

    if(!dir.exists(groups_fold_thresh_up)) dir.create(groups_fold_thresh_up, recursive=T)
    write.table(filtered$genes[filtered$log2FoldChange>0], paste0(groups_fold_thresh_up,"/up_genes_list_",files,"_thFC",log2FC_threshold,"_thPval",padj_threshold,".txt"), quote = F, row.names = F, col.names = F)

    if(!dir.exists(groups_fold_thresh_down)) dir.create(groups_fold_thresh_down, recursive=T)
    write.table(filtered$genes[filtered$log2FoldChange<0], paste0(groups_fold_thresh_down,"/down_genes_list_",files,"_thFC",log2FC_threshold,"_thPval",padj_threshold,".txt"), quote = F, row.names = F, col.names = F)


  }
}