Convert HiC-Pro results to BEDPE format
The 3 column sparse upper triangular matrix from HiC-Pro.
The BED file containing the mappings for for the matrix.
HiC-Pro will produce a .matrix file and a .bed file as the final aligned product of the alignment process. These files should be read into R using read.table() or similar and then entered as the mat and bed inputs to this function. The function will convert the data into a format useable for HiCcompare. The cis matrices in the results can be directly input into create.hic.table() as sparse matrices.
A list with two items. Item 1, "cis" contains the intra-chromosomal contact matrices, one per chromosome. Item 2, "trans" contains the inter-chromsomal contact matrix.
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