[BioC] ChiPseq input files?

[Jonathan Cairns]

Hi John,

I'm afraid I don't understand your question. It sounds like you are trying to bin the reads? This shouldn't be necessary, as both packages do this for you. Was that your intended query?

Jonathan
________________________________________
From: John linux-user [johnlinuxuser at yahoo.com]
Sent: 17 September 2012 15:59
To: Jonathan Cairns; bioconductor at r-project.org
Subject: Re: [BioC] ChiPseq input files?

Hi Jonathan,

Thanks for your response and codes. That saves me a lot of time to look over the webs. Your answers are great!  but if I try to create a table using python or other scripts and then input the table to R for statistics, how can I decide the range (e.g. start and end) when I count the reads in each position across the chromosomes/genome? Can you give me more suggestions? Thanks.

Best,

John

________________________________
From: Jonathan Cairns <Jonathan.Cairns at cancer.org.uk>
To: John linux-user <johnlinuxuser at yahoo.com>; "bioconductor at r-project.org" <bioconductor at r-project.org>
Sent: Monday, September 17, 2012 10:38 AM
Subject: RE: [BioC] ChiPseq input files?

Hi John,

I would try the Rsamtools package. You'd need something like this (warning, untested code):

library(Rsamtools)

bamFile = "path/to/Bamfile.bam"
p <- ScanBamParam(what=c("rname", "strand", "pos", "qwidth"))
bam <- scanBam(bamFile, param=p)[[1]]

BayesPeak accepts data.frames or RangedDatas. I would suggest the easiest thing to do is construct a RangedData:

library(IRanges)
IR <- IRanges(start=bam[["pos"]], width=bam[["qwidth"]])
x <- RangedData(ranges=IR, strand=bam[["strand"]], space=bam[["rname"]])

chipseq accepts GRanges by preference:

library(GenomicRanges)
y <- GRanges(seqnames=bam[["rname"]], ranges=IR, strand=bam[["strand"]])

There may be a faster/cleverer way of doing it, but this should work.

Jonathan


________________________________________
From: bioconductor-bounces at r-project.org<mailto:bioconductor-bounces at r-project.org> [bioconductor-bounces at r-project.org<mailto:bioconductor-bounces at r-project.org>] On Behalf Of John linux-user [johnlinuxuser at yahoo.com<mailto:johnlinuxuser at yahoo.com>]
Sent: 17 September 2012 15:04
To: bioconductor at r-project.org<mailto:bioconductor at r-project.org>
Subject: [BioC] ChiPseq input files?

Hi,

I am wondering how to simply prepare the input files for R BayesPeak and chipseq packages, assuming BAM files already generated by BWA and samtools.  Thanks.

John
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