Question: Label points on DESeq2 MA plot with interval list
0
gravatar for rbronste
29 days ago by
rbronste60
rbronste60 wrote:

I am wondering whether it is possible to label/color individual points on a DESeq2 MA plot based on a list of intervals? Thanks.

annotation deseq2 maplot • 65 views
ADD COMMENTlink modified 29 days ago by Michael Love26k • written 29 days ago by rbronste60
Answer: Label points on DESeq2 MA plot with interval list
1
gravatar for Michael Love
29 days ago by
Michael Love26k
United States
Michael Love26k wrote:

Yes it’s possible but it would involve basic use of other packages, eg GenomicRanges to find the genes that overlap. You’ll need the ranges of the genes. We have created the tximeta package to assist with this if you have Salmon quantifications. Or if you’ve used featureCounts or htseq you can create ranges from the genes used for the counting process.

ADD COMMENTlink written 29 days ago by Michael Love26k

Thanks for the info Michael, my situation is actually much simpler than that since Im using DESeq2 to look for differential peaks in ChIP-seq data, so basically I am interested in taking some differential peak calls from one dataset and mapping it onto the MAplot of another, to see overlap in that fashion - mostly just interested in coloring the dots to see distribution, don't need labels.

ADD REPLYlink written 29 days ago by rbronste60
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