Open jiangshan529 opened 1 year ago
Hi there,
Have you tried the sync_indices()
function?
E.g.
explist <- sync_indices(list(WT, KO))
apa <- APA(explist, bedpe = peaks)
apa <- APA(explist, bedpe = peaks)
Hi, another error: 'Error in value[[1L]] : subscript out of bounds'
I made a typo, I meant bedpe = peak
instead of peaks
.
Is it specifically APA()
that gives this error, or do others give this error as well?
If it is just APA()
, can you show me the output of head(peak)
?
Hi, I know there's a typo, so I changed it. APA runs successfully. head(peak) shows this: V1 V2 V3 V4 V5 V6 1 chr19 3290000 3300000 chr19 3440000 3450000 2 chr19 8570000 8580000 chr19 8680000 8690000 3 chr16 42160000 42170000 chr16 44060000 44070000 4 chr16 44760000 44770000 chr16 45090000 45100000 5 chr16 44760000 44770000 chr16 45630000 45640000 6 chr16 62940000 62950000 chr16 64740000 64750000
Ah good, so this issue appears to be resolved then?
Ah good, so this issue appears to be resolved then? no, the same error:
apa <- APA(explist, bedpe = peak) Error in value[[1L]] : subscript out of bounds
Ah good, so this issue appears to be resolved then?
Hello, there is still such an error: apa <- APA(explist, bedpe = peak) Error in value[[1L]] : subscript out of bounds
Yeah sorry I don't know what causes the error, I cannot reproduce this on my end.
the error "subscript out of bounds" in this package is often caused by chromosome name is inconsistent between files, i.e. "1" vs. "chr1"
Thanks @Moonriver1988, that seems like a reasonable thing to check against. I'll see what I can do to give a more friendly error in this case.
Hello, I have two hic files, I read them to R using the codes:
and when I run APA like this:
there is an error:
So how to deal with this? Thanks!