hicpro2bedpe {HiCcompare} | R Documentation

## Convert HiC-Pro results to BEDPE format

### Description

Convert HiC-Pro results to BEDPE format

### Usage

    hicpro2bedpe(mat, bed)

### Arguments

`mat` | The 3 column sparse upper triangular matrix from HiC-Pro.
`bed` | The BED file containing the mappings for for the matrix.

### Details

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.

### Value

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.

### Examples

    ## 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)

[Package HiCcompare version 1.9.0 Index]