plotReadPairCoverage: Plot read-pair coverage profile per breakpoint

plotReadPairCoverageR Documentation

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