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dozmorovlab / TADCompare

Package for analysis and characterization of differential TADs
https://dozmorovlab.github.io/TADCompare/
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nxn matrix #3

Closed BenxiaHu closed 4 years ago

BenxiaHu commented 4 years ago

Hi, my matrix was made by HiC-Pro. And then I converted the matrix to nxn format. image

bed_coords1 = bind_rows(SpectralTAD(input, chr = "chrY", levels = 3)) Error in is.finite(cont_mat) : default method not implemented for type 'list' I got this error. Do you know what is wrong?

mdozmorov commented 4 years ago

First, your matrix has all zeros. Something went wrong there. Check the Input Data vignette.

Second, check the TAD comparison between two conditions vignette how the data should look like. It seems your row- and column names are incorrectly formatted, or the class of your object is incorrect.

BenxiaHu commented 4 years ago

Thanks. Now I can run TADCompare successfully. But I still have one question: image TADCompare does not output the TAD coordinates. Do you know how to output the regions of TADs? Best,

mdozmorov commented 4 years ago

The "Boundaries" column has the coordinates of boundaries for a given chromosome. TADCompare detects changes in boundaries, then, visualizing specific regions for a pair of samples will help to judge how individual TADs change. Check Visualization of TADCompare Results

mdozmorov commented 4 years ago

@benxiahu, closing this issue due to inactivity. Please, ask if you have any other questions.