error when processing dense matrix

[musiccccc]

Dear Prof. HenrikBengtsson,

When I was processing a dense matrix, which have about 50000 rows, with topdom, it failed. Here is the error message:
Error in seq.default(from = 1 + (n_bins * i), to = n_bins * n_bins, by = 1 + :
'to' must be a finite number
Calls: TopDom -> seq -> seq.default
In addition: Warning message:
In n_bins * n_bins : NAs produced by integer overflow
Execution halted

It seems that the type of n_bins is integer, and max number of interger in R is 2*10^9. So, what should I do in this situation?
Looking forward to your helpful reply.

Best,
Qiang

[HenrikBengtsson]

Please see Issue #11

EDIT 2019-10-08: Linking to Issue #11 (was comment in #9)

[JSegueni]

Hey @musiccccc,
I posted an edited version of TopDom to overcome the issue you mentioned, that I also faced in my high-resolution Hi-C matrices.
You can find it here: https://github.com/JSegueni/TopDom.
Hopefully, this can help you !
Best,
Julie.