GreenleafLab
MatrixGeneExpression.R force parameter not properly in if
In MatrixGeneExpression.R there is an error of applying the force
It does not run when force is TRUE but runs if FORCE is false
seqRNA <- paste0(unique(seqnames(seRNA)))
if(sum(seqRNA %in% paste0(seqnames(chromSizes))) <= 0.5 * length(seqRNA)){
if(force){
stop(paste0("Detected less than 50% of seqnames for seRNA in chromSizes! Are you sure the seqnames of your seRNA are correct?!"))
}else{
message(paste0("Detected less than 50% of seqnames for seRNA in chromSizes! Continuing since force = TRUE!"))
}
Hi @eliascrapa! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.
Thanks for the heads up @eliascrapa, I'll try reproducing on my end but probably won't be until eow.
