addDoubletScores

[pengxin2019]

Hi there,
I recently noticed that the geneAnnotation object I have used for createArrowFiles is not as good as I expected since the number of transcript in the TxDb.Sscrofa.UCSC.susScr11.refGene is much less than I thought. I am wondering which information is based on for the addDoubletScores function. Is it based on the fragment/peaks information or the genescore (transcript or gene) information? I read through the full tutorial of ArchR and did not see this info. If it is based on the fragment/peaks, I can still use the detected doublet result at least.

Thanks

[rcorces]

By default, doublet scores are based on fragments (tiles) information because useMatrix = "TileMatrix" is the functions default.