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HenrikBengtsson / TopDom

R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes
https://cran.r-project.org/package=TopDom
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error when processing dense matrix #10

Open musiccccc opened 5 years ago

musiccccc commented 5 years ago

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 commented 5 years ago

Please see Issue #11

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

JSegueni commented 2 years ago

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.