getHIContactCounts: Construct HIC contact matrix.

In daewoooo/primatR: What the Package Does (TODO)

Construct HIC contact matrix.

Description

This function imports HIC reads and construct contact matrix based on user defined resolution or a number of required genomic bins.

Usage

getHIContactCounts(
  bamfile,
  region = NULL,
  min.mapq = 10,
  nbins = NULL,
  resolution = NULL,
  bsgenome = NULL
)

Arguments

bamfile	Bamfile with aligned reads.
region	If only a subset of the genomic regions should be loaded.
min.mapq	Minimum mapping quality when importing from BAM files.
nbins	A number of required bins to split selected genomic region into.
resolution	A vector of genomic bin sizes for which contact counts will be constructed and plotted.

Value

A data.frame object with HiC contact counts between two genomic region in each row.

Author(s)

David Porubsky

daewoooo/primatR documentation built on March 28, 2024, 6:41 a.m.