Question: Quantifying peaks corresponding to a purticular feature
0
gravatar for snigdhapola
4.4 years ago by
CRRao AIMSCS, India
snigdhapola0 wrote:

Hi,

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

 

Thanks,

Snigdha.

chipseeker • 714 views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by snigdhapola0
Answer: Quantifying peaks corresponding to a purticular feature
2
gravatar for Guangchuang Yu
4.4 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

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?

ADD COMMENTlink written 4.4 years ago by Guangchuang Yu1.1k
Answer: Quantifying peaks corresponding to a purticular feature
0
gravatar for snigdhapola
4.4 years ago by
CRRao AIMSCS, India
snigdhapola0 wrote:

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 ?

ADD COMMENTlink written 4.4 years ago by snigdhapola0

how do you calculate the pvalue?
 

ADD REPLYlink written 4.4 years ago by Guangchuang Yu1.1k

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 ?

ADD REPLYlink written 4.3 years ago by snigdhapola0
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