Unable to compare compartment_score with .hic files loaded

[bharaths24]

Hi, I had contacts loaded from a juicer .hic files of different conditions. Upon using compartment_score() for the 2 conditions I get the following error:

Error: Indices of experiment(s) 2 are not equal to indices of experiment 1

I see that the IDs and MAT entries in the 2 files are not of the same number. I am not sure why this would be so and am not sure how to go ahead. Any ideas as to how to proceed would be much appreciated. Thank you very much

[teunbrand]

You can use sync_indices(list(exp1, exp2)) to match up the indices between multiple experiments at the same resolution.

[bharaths24]

Hi, Thank you for the reply. Upon using the synched file for compartment_score in the following way

CS_out = compartment_score(list(synched)

I get the following error:

Error in if (attr(explist[[1]], "resolution") <= 19999) { : argument is of length zero

Thank you

[teunbrand]

If synched <- sync_indices(list(exp1, exp2)) then synced is already a list of experiments. The first argument in comparment_score() accepts an experiment or list of experiments, but not a list of a list of experiments (which I think you might be doing). Here is my attempt at reproducing the problem:

library(GENOVA)
library(data.table)

exp1 <- exp2 <- get_test_data("150k")

# Make exp2 out of sync by making a gap
expnames(exp2) <- "test2"
exp2$IDX$V4[500:664] <- exp2$IDX$V4[500:664] + 5
exp2$MAT <- exp2$MAT[V1 >= 500, V1 := V1 + 5]
exp2$MAT <- exp2$MAT[V2 >= 500, V2 := V2 + 5]
exp2$IDX$V3 <- exp2$IDX$V3 - 1

# Reproduce error
cs <- compartment_score(list(exp1, exp2))
#> Error: Indices of experiment(s) 2 are not equal to indices of experiment 1

# Synchronise indices
synced <- sync_indices(list(exp1, exp2))

# Error fixed
cs <- compartment_score(synced)
print(cs)
#> A GENOVA 'CS_discovery' object involving the following 2 experiment(s):
#> 'Hap1_WT_150k', 'test2' at a resolution of 150 kb.
#> 
#> Contains the following slots:
#>  - compart_scores:   A 664 x 6 data.frame containing unsigned compartment scores.
#> 
#> 2 centromeres spanning a total of 169 bins have been ignored.

^{Created on 2021-05-29 by the reprex package (v1.0.0)}