Hichipper Inter-chromosomal Loop Statistics

[bdecker01]

Hello Hichipper Software Programmers,

I am using your software to analyze some Hi-C / Hi-ChIP data for a research project I am working on, and I am wondering if there is a way to output this same "per-loop FDR measures from the loop proximity bias correction algorithm originally implemented in Mango and presented in the same format" that is output for 'interactions.all.mango' intra-chromosomal loops, for the inter-chromosomal loops results, or if some similar statistics can be easily applied post run on the '.inter.loop_counts.bedpe' output files.

Thanks for the help! Brandon

[caleblareau]

Hi Brandon,

I can see why this would be of interest, but it's hard to imagine how to make a statistic that would be applicable here. Every statistic for computing an FDR value would be reliant on some background model, which for intrachromosomal interactions is a function of genomic proximity. It's hard for me to imagine what an appropriate background model is for interchromosomal interactions.

To these ends, I'd recommend just using the raw counts between loci as I don't see any reason why they would be biased for any pair of points? You could compute an empirical distribution function to attain something resembling a p-value on the raw counts.

Or do you have an idea of how one could create a background model?

[bdecker01]

Hello Caleb,

Thank you for the advice, I computed the probability for the scores based on their empirical distribution and it looks like that gives me a pretty reasonable statistical output. I am still trying a few other different approaches to determine statistical significance for the interchromosomal interactions, but I will let you know if I find some other appropriate ways to determine it.

Thanks again for the help! Brandon