compartment_score

[knight-hzj]

Hi， When I try to do compartment_score, I got the error like this: Indices of experiment(s) 2 are not equal to indices of experiment 1. I also check my two .hic files, they are not equal on MAT and IDX, Could you please let me know how to figure this out ?

Thanks!

[teunbrand]

Hi there,

If the experiments were loaded at the same resolution but from two files, one could use sync_indices() to match up the indices.

Cheers

[knight-hzj]

Thanks so much for you quick reply, the problem is solved with your suggestion. But I got another issue when I continue to do the compartment_score, the error like this: centromeres of experiments are probably incompatible. For my input .hic files, they are both aligned from Juicer. centromeres of two files are same, please see below, Much appreciated! chrom start end 1: 1 1216 1425 2: 10 2886 2916 3: 11 4365 4395 4: 12 5548 5576 5: 13 7216 7472 6: 15 8397 8400 7: 16 9562 9671 8: 17 10335 10363 9: 18 11079 11108 10: 19 11952 11981 11: 2 13221 13249 12: 20 14993 15022 13: 21 15377 15407 14: 22 15754 15754 15: 3 17006 17034 16: 4 18577 18605 17: 5 20456 20484 18: 6 22385 22414 19: 7 24089 24117 20: 8 25539 25567 21: 9 27037 27218 22: X 28563 28592 23: Y 29793 30091

[knight-hzj]

Hi, I am sorry except the question above, I also got another issue, when I tried to some analysis, such as insulation_domainogram() or cis_trans (), got error like this: Error in value[[1L]] : subscript out of bounds. So, may I kindly ask how to solve problem like this? Thank you!

[Lucas446]

Hi,

I have the same issue as @knight-hzj (not equal indices...), but when I wnat to do sync_indices function I get:

synched <- sync_indices(list(St10_25kb_cool, St14_25kb_cool, St14esc_25kb_cool))

Error in `:=`(c("start", "end"), list(match[start], match[end])) : 
  Check that is.data.table(DT) == TRUE. Otherwise, := and `:=`(...) are defined for use in j, once only and in particular ways. See help(":=").

Any ideas why ?

Best, Tanguy