get_contacts_matrix: Make a contact matrix from HiC data

In qenvio/hicutils:

Description

This function takes a HiC-BAM file and creates a contact map as a sparse_ matrix with dimnames corresponding to the genomic bins

Usage

get_contacts_matrix(inbam, resolution, region = NULL, pos, whole = F,
  filtin = 0, filtex = 783)

Arguments

inbam	HiC-BAM file
resolution	Desired resolution (bin size)
region	Region of interest following the format chr|chr:start-end. If NULL, take the entire genome
pos	A vector with the genomic position IDs to be included in the output. It can be the column of the output from make_bins
whole	Logical indicating if the entire available genome should be retrieved (rectangular contact map) or only the region of interest indicated with region (square contact map). It should be consistent tih pos argument
filtin	Integer value indicating the required bits for the HiC-BAM FLAG (include the corresponding contacts in the output)
filtex	Integer value indicating the excluded bits for the HiC-BAM FLAG (exclude the corresponding contacts in the output)

Value

A named sparse_matrix containing the number of contacts per pair of genomic bins at the requested region

Examples

plot(0)

qenvio/hicutils documentation built on May 26, 2019, 11:35 a.m.