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dozmorovlab / HiCcompare

Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices
https://dozmorovlab.github.io/HiCcompare/
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exclude.regions #18

Closed fgualdr closed 2 years ago

fgualdr commented 4 years ago

In create.hic.table the code should check if is a data.frame OR a Grange and not an AND e.g. if (!is(exclude.regions, "data.frame") & !is(exclude.regions, "GenomicRanges")) vs if (!is(exclude.regions, "data.frame") | !is(exclude.regions, "GenomicRanges"))

fgualdr commented 4 years ago

I'm correcting myself. Code is correct with the &. I am getting an issue when running create.hic.table with mapply and I want to add the exclude.regions. Even though is a data.frame I keep getting the error: "Enter a data.frame or GenomicRanges object for exclude.regions" I don't understand why

mdozmorov commented 4 years ago

Can you provide R objects (save(list = c(...))) and the code that uses them and causes an error?

A simple workaround would be to analyze the data with all regions, and exclude regions from the final results. But please, provide more details, we need to debug it.

CC'ing @jstansfield0 in case he may have some suggestions.

mdozmorov commented 2 years ago

Closing due to inactivity.