Open dottercp opened 1 year ago
Hi, thanks for reporting this. Until I fix it, what you can do is run the aggregation separately, e.g. this should reproduce what you're trying to do:
sce.ag <- aggregateFeatures(sce, k=50)
sce.ag <- scDblFinder(sce.ag, processing="normFeatures",
knownDoublets = (sce.ag$ident == doublet_sample))
sce$scDblFinder.score <- sce.ag$scDblFinder.score
As a note, I'm also exploring now doing it with a high k (e.g. 500) and with the normal processing, e.g.:
sce.ag <- aggregateFeatures(sce, k=500)
sce.ag <- scDblFinder(sce.ag)
Although I still haven't tested systematically that it's better...
Thanks a lot for the quick answer and the workaround!
Dear developers,
I'm working with multiplexed (CMO) scATAC-seq data (one 10X-run has 6 samples) which gives me information on known doublets from overlap of hashtags. When using the
scDblFinder
function for this data I wanted to provide these doublets asknownDoublets
and aggregate features as recommended in the vignette. However, I found that this combination of parameters does not work and throws an error (see below). After some debugging I found that the source of the issue might be that the splitting of the dataset in known doublets (sce.dbl
) and others (sce
) is performed before aggregation which leads to a mismatch of row names between the two subsets.MRE -- Minimal example to reproduce the bug
Traceback
Session info