R/RemoveCellCycle.R

In lyc-1995/DoubletDeconSeurat: Seurat wrappers with DoubletDecon

#' Remove Cell Cycle
#'
#' This function looks for enrichment of cell cycle gene expression clusters and removes those genes.
#'
#' @param data Processed data from Clean_Up_Input.
#' @param species Species as scientific species name, KEGG ID, three letter	species abbreviation, or NCBI ID.
#' @param log_file_name used for saving run notes to log file
#'
#' @return data - data.frame with cell cycle gene cluster removed.
#'
#' @keywords cell cycle KEGG
#'
#' @export
#'
RemoveCellCycle <- function(
  data,
  species,
  log_file_name
) {
  #load in table of species names
  data(CCtable)

  IDtype <- which(apply(CCtable, 2, function(x) any(grepl(paste0('\\<', species, '\\>'), x))))
  ccclust <- 0
  if (IDtype > 0) {
    #Find the row containing species name information for the provided species
    IDrow <- which(apply(CCtable, 1, function(x) any(grepl(paste0('\\<', species, '\\>'), x))))

    for (rowCluster in 1:(length(x = unique(data[2:nrow(x = data), 1])))){
      genes <- rownames(x = subset(data[2:nrow(x = data), ], data[2:nrow(x = data), 1] == rowCluster)) #get the genes for the row cluster
      sink('/dev/null') #hides mygene output
      geneEquiv <- mygene::queryMany(genes, species = CCtable[IDrow, 4], fields = 'entrezgene', scopes = c('symbol', 'alias', 'name'), return.as = 'DataFrame') #convert to entrezid
      sink()
      entrezIDs <- geneEquiv@listData$entrezgene #grab entrezids
      KEGGresults <- enrichKEGG(entrezIDs, organism = CCtable[IDrow, 3], pvalueCutoff = 0.05, pAdjustMethod = 'BH', qvalueCutoff = 0.1) #submit entrezids for KEGG enrichment
      #look to see if "Cell Cycle is in the list"
      KEGGresultsCC <- nrow(x = subset(KEGGresults, KEGGresults$Description == 'Cell cycle'))
      if (KEGGresultsCC > 0) {
        data <- subset(data, (data[,1] != rowCluster | is.na(data[, 1]))) #Remove the cell cycle cluster, is.na() required so we don't lose the "column_clusters-flat" row
        ccclust <- ccclust+1
      }
    }
  }
  cat(paste0(ccclust, ' cell cycle clusters removed'), file = log_file_name, append = TRUE, sep = '\n')
  message(paste0(ccclust, ' cell cycle clusters removed'))
  return(data)
}