Entering edit mode
Xiaohui Wu
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280
@xiaohui-wu-4141
Last seen 10.3 years ago
Hi all,
I'm using chipseq package to find peak in my count data.
The R code is like this:
ranges = IRanges(start=tag$start, end=tag$end,width=tag$end-
tag$start+1, names = tag$tag_id)
gr <- GRanges(seqnames = seqnames,ranges = ranges,strand =strand)
gr.ext <- resize(gr, width = 200)
cov <- coverage(gr.ext)
islands <- slice(cov, lower = 1)
thd=peakCutoff(cov, fdr = 0.05)
peaks <- slice(cov, lower = thd)
I found that the processing is not I expected, where tag was expanded
to fragment and then calculate coverage. For my data, the data format
is like: <chr,strand,tag_start,tag_end,count>, where count is the
count for that tag.
How to use the "count" information to calculate the coverage?
Otherwise I think I need to repeat the tag for 'count' times and the
do coverage, this is too trouble.
Thank you!
Regards,
Xiaohui
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