Closed deWitLab closed 4 years ago
I'm not sure what you mean with loop anchor list? Is it a list of BEDPE-formatted data.frames, a list of pre-converted anchor objects or simply an unlisted/flat BEDPE-formatted data.frame?
Unlisted BEDPE formatted data.frame (6 columns).
I can't reproduce this error, I tried the following:
scrambled <- bedpe[sample(nrow(bedpe)),]
dim(bedpe)
# [1] 6976 6
# Run APAs
apa_standard <- APA(list(exp, exp2), bedpe = bedpe)
apa_scrambled <- APA(list(exp, exp2), bedpe = scrambled)
# Extract raw data
standard <- apa_standard$signal_raw[[1]]
scrambld <- apa_scrambled$signal_raw[[1]]
# Order identically
standard <- standard[order(rownames(standard)),,]
scrambld <- scrambld[order(rownames(scrambld)),,]
# Check equivalence
identical(standard, scrambld)
# [1] TRUE
I'm closing this for now, if it is more clear how to make this error occur, please feel free to reopen.
APA function seems to fail when an unsorted loop anchor list is used. At least ‘Error: No suitable anchors left after out-of-bounds filtering.’ can be solved by sorting loop anchor list.