getHIContactCounts: Construct HIC contact matrix.

View source: R/processHICdata.R

getHIContactCountsR Documentation

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 Oct. 22, 2024, 9:41 p.m.