Label points on DESeq2 MA plot with interval list
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rbronste ▴ 60
@rbronste-12189
Last seen 23 months ago

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

deseq2 maplot annotation • 197 views
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@mikelove
Last seen 12 hours ago
United States

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.

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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.

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