Using DEXSeq with bam files

[Jetse]

Hello everyone,

I'm working with the programming language R and want to use DEXSeq.
First I executed tophat on my reads to map them against a human reference genome.
In R I created a function to load the bam file of tophat:

getCounts <- function( alignmentName, run, tx ){
  fileName <- paste( "/pathToDir/", alignmentName, "/", alignmentName, "run", run, ".merged.bam", sep="" ) #my directory structure
  alignment <- readBamGappedAlignments( fileName )
  newReadNames <- gsub( "([0-9(MT|X|Y)])" , "chr\\1" , rname( alignment ) )
  alignment <- GRanges( seqnames = newReadNames, ranges = IRanges( start = start( alignment ),													   end=end(alignment)), 														   strand=strand(alignment))
  alignmentCounts <- suppressWarnings( countOverlaps( tx,alignment ) )
  return( alignmentcounts )
}

I call this function for each replicate and this gives me a dataset with raw counts. These raw counts I get with these code:

txdb <- makeTranscriptDbFromUCSC( genome='hg19', tablename='ensGene' )
tx_by_exon <- transcriptsBy( txdb, 'exon' )
tx_by_gene <- transcriptsBy( txdb, 'gene')
pos1_1 <- getCounts( "pos", 1, tx_by_exon)
pos1_2 <- getCounts( "pos", 2, tx_by_exon)
neg1_1 <- getCounts( "neg", 1, tx_by_exon)
neg1_2 <- getCounts( "neg", 2, tx_by_exon)

Then I create a dataframe with all counts:

allCounts <- data.frame( pos1_1 = pos1_1, pos1_2 = pos1_2, neg1_1 = neg1_1, neg1_2 = neg1_2, )

And a dataframe to describe the design:

design <- data.frame(
		row.names = colnames(allCounts),
		condition = c( "pos", "pos", "neg", "neg" ),
		libType = c( "paired-end", "paired-end", "paired-end", "paired-end"))

And now I stuck...
To create a exonCountset, I want to use this function:

data <- newExonCountSet(allCounts, design, ?,rownames(allCounts))

My question is, how do I get the gene IDs of these counts?
And another question I have is whether it is possible to use the tx_name instead of the tx_id.