Description Usage Arguments Details Value Examples
Convert HiC-Pro results to BEDPE format
1 | 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. |
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.
1 2 3 4 5 6 7 8 | ## Not run:
# read in data
mat <- read.table("hic_1000000.matrix")
bed <- read.table("hic_1000000_abs.bed")
# convert to BEDPE
dat <- hicpro2bedpe(mat, bed)
## End(Not run)
|
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