Motif matching when using mouse data
Opened this issue · 6 comments
Hi! I was running into an issue when selecting TFs in my mouse data, because the motif names did not match many genes in the gene exp data. I ended up altering the SelectTFs and GetTFGeneCorrelation code to
rownames(trajMM) <- stringr::str_to_title(object@assays[[atac.assay]]@motifs@motif.names)
(although maybe a biomaRt matching or something would be more accurate) and am getting better results, so I thought I'd note it!
Thanks for reporting this point. Indeed, we only tested the function using human data, where the gene names are all capitalized.
Using biomatRt is absolutely better and I will add it to our TODO.
Thanks,
Zhijian
Hi! I was running into an issue when selecting TFs in my mouse data, because the motif names did not match many genes in the gene exp data. I ended up altering the SelectTFs and GetTFGeneCorrelation code to
rownames(trajMM) <- stringr::str_to_title(object@assays[[atac.assay]]@motifs@motif.names)(although maybe a biomaRt matching or something would be more accurate) and am getting better results, so I thought I'd note it!
Dear @AmandaKedaigle
I'm trying to make scMega works and I encounter the same problem as you did: the matrix names are not recognized. I would like to do the same modification you did (modifying the rownames(trajMM) code but I'm truly lost about how to do it, I can't find the file containing the selectTFs function in my ScMega R libs. Can you help me ?
Best regards
David
Hi David! If you're using RStudio you can write View(function_name) to see code for a function in a loaded package (or View(package_name::function_name). I believe that outside of RStudio you can still see the code with just the function name, no parentheses. I just copied the code for those functions into a new script, altered that line, and then loaded my new functions overtop of the package ones. Hope this helps!
Hi Amanda
Thanks a lot ! It's working :)
Just to know, did you had incompatibility problems between ScMEGA and seurat V5 (if you use seurat that is ?) I have this error poping up : Error in GetAssayData():
! No layers are found
Best and thanks again :)
David
I was using Seurat, but was still on v4 - didn't run into that one!
the V5 is a bit annoying with lots of incompatibility !
Thanks a lot for your help !
Best
David