plotReadPairCoverage: Plot read-pair coverage profile per breakpoint

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

Plot read-pair coverage profile per breakpoint

Description

This function takes as an input aligned read-pairs in BAM and plots coverage profile per breakpoint. Breakpoint positions are stored as part of a readName. e.g. readName__chr1-109148195-109148196__chr1_invDup_gorilla_roi4_1

Usage

plotReadPairCoverage(
  bamfile,
  mapq = 10,
  filt.flag = 0,
  min.read.len = 5000,
  plot.ambig = FALSE,
  plot.pairs = FALSE,
  blacklist = NULL,
  view.range = 1e+05
)

Arguments

bamfile	Bamfile with aligned reads.
mapq	Minimum mapping quality when importing from BAM files.
filt.flag	Filter out reads with given flag.
min.read.len	Minimum length of mapped reads to import.
plot.ambig	Bamfile with aligned reads.
plot.pairs	Bamfile with aligned reads.
blacklist	A GRanges-class object of regions to exclude reads from.
view.range	Bamfile with aligned reads.

Value

A ggplot object.

Author(s)

David Porubsky

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