Question: Chip-seeker heatmap around the peak centers
gravatar for Jingyue
3 months ago by
United States
Jingyue30 wrote:


I'm wondering how to plot the heatmap around the peak center in ChIPseeker? Can I plot 3 samples in 1 plot? Do I need a merged peak file?

Here is the code I use to plot around TSS, but don't know how to do it for peak center. Thank you!

promoter <- getPromoters(TxDb=txdb, upstream=1000, downstream=1000)
tagMatrixList <- lapply(files, getTagMatrix, windows=promoter)
chipseeker R • 209 views
ADD COMMENTlink modified 11 weeks ago by zx87548.7k • written 3 months ago by Jingyue30

hi Jingyue,

In your example you plot the profile of ChIP peaks binding to TSS region (distance of peaks from TSS).

What is exactly the other plot, you are talking about?

Using the center of the peak as reference and plot the signal of bam or bigwig file?

p.s. sorry editors, I accidentally used answer button

ADD REPLYlink modified 3 months ago • written 3 months ago by 2nelly170

I would like to plot the ChIP peaks binding enrichment around its binding center.

I plotted this using deeptools, but would like to see how it look like in ChIP-seeker.

ChIP-seq inputs are peak.bed files, so I don't think is over bam/bigwig files

Thank you!

ADD REPLYlink written 3 months ago by Jingyue30
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