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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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error addPmatToSnap(x.sp) #142

Open hjack123 opened 4 years ago

hjack123 commented 4 years ago

x.sp = addPmatToSnap(x.sp) Epoch: reading cell-peak count matrix session ... Error in mcols(x, use.names = FALSE)[[name]] : this S4 class is not subsettable can anyone help with this - kind of emergent analysis...much appreciated...

hjack123 commented 4 years ago

Would be much appreciated if anyone has some ideas.... by repeating snap-del session-name PM and snap-add-pmat didnt help

hjack123 commented 4 years ago

x.sp@feature GRanges object with 642098 ranges and metadata : Error: subscript is a NSBS object that is incompatible with the current subsetting operation Error during wrapup: cannot get a slot ("slots") from an object of type "NULL"

hjack123 commented 4 years ago

I solved it by rerunning addBmatToSnap(x.sp) but still would like to know why it happened.... also after adding pmat, the x.sp object became ~140GB. which is extremely huge. I run make binary for both bmat and pmat. is it (the size) something expected? thank you!!

hjack123 commented 4 years ago

the reason x.sp being huge was I did x.sp@metaData$DEpeak=DARs....