Hi there,
may be I am missing something obvious in my code.
I extracted information from a bam file on 11 regions.
when I calculate the coverage on one of these regions, I get a vector which is
much longer than the number of bases of the region itself.
I tried several times to replicate this problem on a small IRanges object but -
of course - everything was ok.
Anyone has an idea?
that's what I've done:
> regions
chr start end
1 1 195915909 197867662
2 2 1199920 2234892 [...]
scanned my bam within those regions
which=GRanges(regions$chr,IRanges(regions$start,regions$end))
ggf<-scanBam("s_7_1_sequence.txt.novo.rmdup.bam_sorted.bam",
param=ScanBamParam(which=which,
what = c("pos", "qwidth"),
flag =scanBamFlag(isUnmappedQuery =FALSE)))
created a summary function, as suggested in the IRanges vignette
summaryFunction<-function(seqname,bamfile,...){
x<-bamfile[[seqname]]
coverage(IRanges(x[["pos"]],width=x[["qwidth"]]))
}
applied to get a list of coverage for each region
seqnames<-names(ggf)
cvg<-lapply(seqnames,summaryFunction,ggf)
names(cvg)=seqnames
then I extracted one of those regions, and computed the vector coverage
areacov<-cvg[["14:20404091-35890861"]]
areacov.vect<-as.vector(areacov)
however
positions=seq(from=20404091,to=35890861,by=1)
> areacov
'integer' Rle of length 35890857 with 445958 runs
Lengths: 20404015 1 1 1 ... 25 121 76
Values : 0 2 5 6 ... 1 0 1
> length(positions)
[1] 15486771
as you can see from here, the Rle has a length of 35890857
even considering that my area is a bit larger, 'cause it gets the reads
positions
> min(ggf[["14:20404091-35890861"]][["pos"]])
[1] 20404016
> max(ggf[["14:20404091-35890861"]][["pos"]])
[1] 35890782
I still have a coverage vector much longer then expected.
I am surely doing something wrong, but the procedure seemed straigthforward.
Any clue to help?
cheers,
Francesco
--------------------------------------
Francesco Lescai, PhD
Research Associate in Genome Analysis
Faculty of Biomedical Sciences, Division of Research Strategy
c/o UCL Cancer Institute, Paul O'Gorman Building
University College London
Gower Street WC1E 6BT London, UK
visiting address: 72, Huntley Street
WC1E 6DE London
email: f.les...@ucl.ac.uk
phone: +44.(0)20.7679.6812
[ext: 46812]
--------------------------------------
_______________________________________________
Bioc-sig-sequencing mailing list
Bioc-sig-sequencing@r-project.org
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
