TopDom is a software tool to ideintify Topological Domains, which are basic builiding blocks of genome structrue. TopDom is computationally very efficient. Using detecting optimal polygon algorithm, TopDom detect topological domains in a linear time. As well as, this tool requires only a single parameter, which enable user to use easily.
Hello,
I am trying to process the matrix file( n x n) with NA for non-interacting regions. However, I am facing an error while reading the matrix with the readHiC function, such as :
Error in readHiC(pathname_1, chr = chr, binSize = 50000) :
all(is.numeric) is not TRUE
However, converting NA to zero resolves the issue, but we observed the output as incorrect, given it produces false positive TADs, due to replacing NA with zero.
Can someone guide me if they have faced the same issue and how you dealt with it? Any comment/suggestion is appreciated. Thank you
Hello, I am trying to process the matrix file( n x n) with NA for non-interacting regions. However, I am facing an error while reading the matrix with the readHiC function, such as : Error in readHiC(pathname_1, chr = chr, binSize = 50000) : all(is.numeric) is not TRUE
However, converting NA to zero resolves the issue, but we observed the output as incorrect, given it produces false positive TADs, due to replacing NA with zero. Can someone guide me if they have faced the same issue and how you dealt with it? Any comment/suggestion is appreciated. Thank you