Hello,

I'd like to identify the peak summit for each peak in a list of ChIPseq
peaks. I've been using IRanges/Genomic Ranges & Rsamtools to read in the BAM
file with mapped reads, seperated reads according to  '+' and '-'
strand-mappings ( & dropped unmapped reads).
I have a predefined list of peak regions that I'm interested in, so I only
take the reads that map to these regions.

x=BAM_data[BAM_data %in% Peak_regions]
x_views=views(coverage(x), Peak_regions)

which gives me an Rle looking like this

           start     end      width
[1] 3114398 3114591   194 [0 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
5 5 5 5 5 5 5 5 5 5 5 5 5 ...]
[2] 3198876 3199070   195 [0 0 0 0 0 0 0 0 0 0 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
3 3 3 3 3 3 3 0 0 0 0 0 0 ...]

Does anybody have some advice on what is the best way to access the coverage
data in this object and find the maximum value/summit?

Many thanks!!
Daniela

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