Quantifying peaks corresponding to a purticular feature
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@snigdhapola-7746
Last seen 8.8 years ago
CRRao AIMSCS, India

Hi,

how to quantify the peaks annotated to a particular genomic region in a particular window size.

 

Thanks,

Snigdha.

chipseeker • 1.2k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 5 days ago
China/Guangzhou/Southern Medical Univer…

A possible solution is define the genomic region as a GRanges object and use the findOverlaps from GenomicFeatures package to get the peaks that overlap with the genomic region. Then you can count the number of peaks.

 

Any idea?

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@snigdhapola-7746
Last seen 8.8 years ago
CRRao AIMSCS, India

It is after we get a count of no of peaks corresponding to a TF or histone mark, say around 3-4kb of  TSS region of a particular gene, do we go by taking an average of -log10(pvalue) of the peaks we obtained in the region or any other way ?

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how do you calculate the pvalue?
 

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No. If we get more than one peak in a given window size, around a gene, for a particular histone modification or transcription factor, any idea if we have to consider peak with max p-value or an average of the p-values of all the peaks in that window size ?

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