Subset does not take Motif positions with it

[skilpinen]

Hi,

Encountered an issue where seurat object having chromatin assay and motif data within it subjected to subset leads to situation where there still is Motif data present in the object but not the @positions data. It becomes NULL in this case.

Original data:

head(Motifs(s.data[["peaks"]])@positions)
GRangesList object of length 6:
$Arnt_MA0004.1
GRanges object with 37214 ranges and 1 metadata column:
seqnames ranges strand | score
|
[1] chr1 3218627-3218632 + | 11.2289
[2] chr1 3218627-3218632 - | 11.2289
[3] chr1 4519629-4519634 + | 11.2289

Then

s.data.subset <-subset(s.data, idents=c("1","2","3","4"))

Then

head(Motifs(s.data.subset[["peaks"]])@positions)
NULL

[timoast]

Thanks for reporting, this should now be fixed on the develop branch

[skilpinen]

Thanks for quick action, confirm as fixed. Closing ticket.