get_contacts_per_bin: Retrieve HiC data per genomic bin

Description Usage Arguments Value Examples

View source: R/get_contacts_per_bin.R

Description

This function takes a HiC-BAM file and creates a nammed vector with the total number of contact per genomic bin

Usage

1
2
get_contacts_per_bin(inbam, resolution, region = NULL, pos, 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 bin column of the output from make_bins

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 vector containing the total number of contacts per genomic bin at the requested region

Examples

1
plot(0)

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