On 03/31/2011 08:32 AM, Cook, Malcolm wrote:
Matt et. al.,
I wonder if a satisfactory resolution to the issue of "the order
changes between the GRanges object and the countBam data.frame
http://www.mail-archive.com/bioc-sig-sequencing@r-project.org/msg01144.html
I am presented with the same issue and poised to tackle it but wondr
if a generic solution emerged from you inquiries& efforts.
Hi Malcolm --
For a reproducible example,
library(Rsamtools)
example(countBam)
which1 <- as(which, "GRanges")
## which2 might be where your data actually starts
which2 <- which1[c(2,1,3)]
values(which2)[["OriginalOrder"]] <- 1:3
param <- ScanBamParam(which=which2)
cnt <- countBam(fl, param=param)
What happens is that ScanBamParam converts its argument to an
IRangesList, using split(ranges(which2), seqnames(which2)). So do the
same for the values and unlist
cntVals <- unlist(split(values(which2), seqnames(which2)))
then cbind coerced values
cbind(cnt, as.data.frame(cntVals))
with
> which2
GRanges with 3 ranges and 1 elementMetadata value
seqnames ranges strand | OriginalOrder
<Rle> <IRanges> <Rle> | <integer>
[1] seq2 [ 100, 1000] * | 1
[2] seq1 [1000, 2000] * | 2
[3] seq2 [1000, 2000] * | 3
seqlengths
seq1 seq2
NA NA
> cbind(cnt, as.data.frame(cntVals))
space start end width file records nucleotides OriginalOrder
1 seq1 1000 2000 1001 ex1.bam 612 21549 2
2 seq2 100 1000 901 ex1.bam 1169 41235 1
3 seq2 1000 2000 1001 ex1.bam 642 22640 3
Martin
Thanks,
Malcolm Cook Stowers Institute for Medical Research -
Bioinformatics Kansas City, Missouri USA
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