get_contacts_per_bin: Retrieve HiC data per genomic bin

In qenvio/dryhic: Some Functions to Handle HiC Data

Description

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

Usage

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

plot(0)

qenvio/dryhic documentation built on March 17, 2020, 8:37 p.m.