R/read.gtf.R

In exomePeak: exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis

# read gtf file
.read.gtf <- function(PARAMETERS){
  # download the annotation
  if ((!is.na(PARAMETERS$GENOME)) & (!is.na(PARAMETERS$UCSC_TABLE_NAME)) & is.na(PARAMETERS$GENE_ANNO_GTF) & is.na(PARAMETERS$TXDB)) {
    op <- options(warn = (-1))
    txdb =makeTxDbFromUCSC(genome=PARAMETERS$GENOME,
                                   tablename=PARAMETERS$UCSC_TABLE_NAME)
    options(op)
  }
  
  # use provided annotation data file
  if (!is.na(PARAMETERS$GENE_ANNO_GTF) & is.na(PARAMETERS$TXDB) ) {
    op <- options(warn = (-1))
    txdb=makeTxDbFromGFF(PARAMETERS$GENE_ANNO_GTF,format="gtf")
    options(op)
  }
  
  # use provided annotation data file
  if (!is.na(PARAMETERS$TXDB) ) {
    txdb=PARAMETERS$TXDB
  }
  
  # try the internet method
  # op <- options(warn = (-1))
  # ID = keys(txdb, "TXID")
  # temp = select(txdb, ID , c(columns(txdb))[c(7:8,12:14)], "TXID")
  # options(op)
  # temp = cbind(temp,"exon")
  # temp=temp[,c(2,7,4,5,3,6,1)]
  # colnames(temp)=c("chr","feature","start","stop","strand","gene","transcript")
  # gtf=temp
  
  colkey <- columns(txdb)
  select_col <- match(c("EXONCHROM","TXID","EXONSTART","EXONEND","EXONSTRAND","GENEID","TXNAME"),colkey)
  op <- options(warn = (-1))
  ID = keys(txdb, "TXID")
  temp = select(txdb, ID , c(columns(txdb))[select_col], "TXID")
  select_col2 <- match(c("EXONCHROM","TXID","EXONSTART","EXONEND","EXONSTRAND","GENEID","TXNAME"),names(temp))
  temp <- temp[,select_col2]
  colnames(temp)=c("chr","feature","start","stop","strand","gene","transcript")
  options(op)
  temp$"feature" <- "exon";
  gtf <- temp

  # return data
  return(gtf)
}