[Bioc-sig-seq] Rsamtools countBam labeling

[Matthew Young]

Hi,

I'm trying to use Rsamtools to bin reads into genes using the countBam  
function.  I have a GRanges object which defines the range of the  
annotation and has additional information in the "elementMetadata"  
field, for example like this:

 > aa
GRanges with 3 ranges and 2 elementMetadata values
     seqnames               ranges strand |     tx_id            tx_name
        <Rle>            <IRanges>  <Rle> | <integer>        <character>
[1]    chr16 [18780546, 18811724]      - |     43866 ENSMUST00000115586
[2]    chr16 [18780546, 18812065]      - |     43865 ENSMUST00000000028
[3]    chr16 [18807449, 18812080]      - |     43868 ENSMUST00000115585

I want to use the countBam function to count the number of reads that  
occur within each annotation range, which I do with the following:

 > countBam("bowtie_aligned.prefix.bam",param=ScanBamParam(which=aa))
   space    start      end width                      file records  
nucleotides
1 chr16 18780546 18811724 31179 bowtie_aligned.prefix.bam       
16         800
2 chr16 18780546 18812065 31520 bowtie_aligned.prefix.bam       
17         850
3 chr16 18807449 18812080  4632 bowtie_aligned.prefix.bam        
2         100

My question is, is there a way to get the "elementMetadata" to come  
along for the ride in the countBam output?  So there'd be another two  
columns in the countBam output, "tx_id" and "tx_name".  The problem is  
that the ranges do not always appear in the same order in the GRanges  
input and the countBam output, so to recover this information it is  
necessary to use match and pull information out of the GRanges object,  
which while doable, is cumbersome.  Is there some built in way to do  
this that I'm overlooking?

Thanks,

Matt


______________________________________________________________________
The information in this email is confidential and intend...{{dropped:4}}