Convert HiC-Pro results to BEDPE format
hicpro2bedpe(mat, bed)
| mat | The 3 column sparse upper triangular matrix from HiC-Pro. |
|---|---|
| bed | The BED file containing the mappings for for the matrix. |
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.
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.
if (FALSE) { # read in data mat <- read.table("hic_1000000.matrix") bed <- read.table("hic_1000000_abs.bed") # convert to BEDPE dat <- hicpro2bedpe(mat, bed) }