R/biotypeOperations.R

In guldenolgun/NoRCE: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

#' Get the biotype of the non-coding genes. It is suitable for the
#' GENCODE gtf files
#'
#' @param gtfFile Path of the input gtf file which contains biotype
#'     information. The gtf file must be provided from the Ensembl
#'     or Gencode site. For space efficiency, gft files should be
#'     in a zip format.
#'
#' @return Tabular form of the gtf file with the required features
#'   such as gene id and biotypes
#'
#' @import readr
#'
#' @examples
#' \dontrun{
#' fileImport<-system.file("extdata", "temp.gtf", package = "NoRCE")
#' gtf <- extractBiotype(gtfFile = fileImport)
#' }
#'
#' @export
#'
extractBiotype <- function(gtfFile) {
  mydata <- read_table(gtfFile, comment = '#', col_names = FALSE)
  r <- sapply(mydata, function(x)
    grepl("gene_type|gene_id", x))
  r <- apply(r,1, any)
  a <- mydata[which(r == TRUE), c(10,14)]
  
  gtf <- apply(a, 2, function(x)
    (gsub("^.* ", "", x)))
  
  gtf <- as.data.frame(gsub("\"", "", gtf))
  
  return(unique(data.frame(gene = gsub("\\..*", "", gtf$X10) ,bio = gsub("\\;.*", "", gtf$X14))))
}

#' Extract the genes that have user provided biotypes. This method is useful
#' when input gene list is mixed or when research of the interest is only
#' focused on specific group of genes.
#'
#' @param gtfFile Input gtf file for the genes provided by the extractBiotype
#'     function
#' @param biotypes Selected biotypes for the genes
#'
#' @return Table format of genes with a given biotypes
#'
#' @examples
#' \dontrun{
#' biotypes <- c('unprocessed_pseudogene','transcribed_unprocessed_pseudogene')
#' fileImport<-system.file("extdata", "temp.gtf", package = "NoRCE")
#' extrResult <- filterBiotype(fileImport, biotypes)
#' }
#'
#' @export
filterBiotype <- function(gtfFile, biotypes) {
  gtf <- extractBiotype(gtfFile = gtfFile)
  all <- data.frame(gene = character(), stringsAsFactors = FALSE)
  for (i in seq_along(biotypes)) {
    index <- which(gtf == biotypes[i], arr.ind = TRUE)
    all <- rbind(all, as.data.frame(gtf[index[, 1], 1]))
  }
  # all <-
  #    as.data.frame(
  #     unlist(apply(unique(all), 2, strsplit, '[.]'))[c(TRUE, FALSE)])
  colnames(all) <- 'gene'
  return(all)
}