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TaoYang-dev / hicrep

R package to evaluate the reproducibility of Hi-C data
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`cool2matrix` has an assumption about the number and the order of chromosomes, but there is no description #72

Open hisakatha opened 1 year ago

hisakatha commented 1 year ago

cool2matrix assumes that the number of chromosomes of your sample is equal to that of the human genome and the order is numerically ascending. https://github.com/TaoYang-dev/hicrep/blob/e485dfa71dc98cadbbda70424084e85a4a94e3b0/R/cool2matrix.R#L26-L43 However, there is no description about the assumption in the ?cool2matrix document. Workaround is using a numerical index of your target chromosome at chr argument of cool2matrix to avoid conversion based on the assumption.