Inclusion of non-human motifs

[sarah-chapin]

Hello,

I am running chromVAR via the wrapper in Signac using the code below:

jaspar24 <- JASPAR2024()
sq24 <- RSQLite::dbConnect(RSQLite::SQLite(), db(jaspar24))
pfm24 <- TFBSTools::getMatrixSet(
  x = sq24,
  opts = list(collection = "CORE", tax_group = 'vertebrates', all_versions = FALSE)
)

atac <- AddMotifs(
  object = atac,
  genome = BSgenome.Hsapiens.UCSC.hg38,
  pfm = pfm24
)

main.chroms <- standardChromosomes(BSgenome.Hsapiens.UCSC.hg38)
keep.peaks <- as.logical(seqnames(granges(atac)) %in% main.chroms)
atac <- atac[keep.peaks, ]

# run chromvar
atac <- RunChromVAR(
  object = atac,
  genome = BSgenome.Hsapiens.UCSC.hg38
)

Although I am including the human genome when adding the motifs and running chromVAR, I still have some mouse motifs that are scored. Do you know why this would be? Furthermore, will the inclusion of the mouse motifs affect the scores for the human motifs?