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