Error in running getRegionUniverse

[MigleMi]

Hello,

I tried the tutorial and it worked, however, when I try to analyse my own data I get this problem, could you help me figure out what should I change?

`output <- chicdiffPipeline(chicdiff.settings)

*** Running getRegionUniverse

Error in if (abs(bait - oe) > s + 1) { : argument is of length zero`

[mspivakov]

Thanks for your interest in chicdiff and sorry to hear you're having issues.

Just checking -

Did you submit the whole Chicago dataset to chicdiff, including non significant interactions? As in, are there interactions in your data that aren't listed in the peak file?

How sparse is your dataset? As in, how many non-zero-read interactions do you have in your Chicago object?

Most likely however we will need to look at your data to pinpoint the problem. Would you be able to share it with us on an ftp or some cloud-based storage?

[MigleMi]

Thank You for quick response, so I looked up at RDa files that I produced with runChicago.R, and yes indeed they contain all interactions, so I could filter only those with score above 5, however I don't know how can I check .chinput files and filter those out I am not really sure how can I see the sparsity of my data but I guess it is very sparse ? what things I could to make it work? not sure if I can share the data

[mspivakov]

Unfortunately if you can’t share the data there’s very little we can do at this stage, as we don’t have a reproducible error report.

You don’t have to share the full dataset though – just a part of it, the smaller the better, that reproduces the problem - and we’ll to look into it for you.

From: MigleMi notifications@github.com Reply-To: RegulatoryGenomicsGroup/chicdiff reply@reply.github.com Date: Monday, 19 August 2019 at 13:21 To: RegulatoryGenomicsGroup/chicdiff chicdiff@noreply.github.com Cc: mspivakov mikhail.spivakov@babraham.ac.uk, Comment comment@noreply.github.com Subject: Re: [RegulatoryGenomicsGroup/chicdiff] Error in running getRegionUniverse (#3)

Thank You for quick response, so I looked up at RDa files that I produced with runChicago.R, and yes indeed they contain all interactions, so I could filter only those with score above 5, however I don't know how can I check .chinput files and filter those out I am not really sure how can I see the sparsity of my data but I guess it is very sparse ? what things I could to make it work? not sure if I can share the data

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