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constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
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quickMarkers specify clusters to compare #109

Closed parkjooyoung99 closed 2 years ago

parkjooyoung99 commented 2 years ago

Hello, I am currently using quickMarkers() for cluster annotation. Though sometimes I need to compare part of the clusters to find the difference between similar cell types. Is there any way to do the same thing with 'FindMarkers(ident.1=3, ident.2=c(6,7,8))' in seurat, except for data subset?

Thank you!

constantAmateur commented 2 years ago

Yes there is, although it's a bit more fiddly. Supposing you would run this to find markers between all cell types:

mrks = quickMarkers(toc,clusters)

then to compare just clusters 6,7, and 8, you would do

w = which(clusters %in% c(6,7,8))
mrks = quickMarkers(toc[,w,drop=FALSE],clusters[w])