plotHICregional: Construct and plot HIC contact matrix.

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

Construct and plot HIC contact matrix.

Description

This function imports HIC reads and plot contact matrix based on user defined resolution.

Usage

plotHICregional(
  bamfile,
  region = NULL,
  min.mapq = 10,
  resolution = 50000,
  highlight.pos = NULL,
  bsgenome = NULL,
  title = 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.
resolution	A vector of genomic bin sizes for which contact counts will be constructed and plotted.
highlight.pos	A vector of genomic positions to be highlighted as horizontal and vertical lines.
title	A character string to be used as a title for each plot.

Value

A ggplot object.

Author(s)

David Porubsky

daewoooo/primatR documentation built on Oct. 22, 2024, 9:41 p.m.