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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