read5endCoverage: Reads Coverage Using 5-end Base

In tengmx/gcapc: GC Aware Peak Caller

Description

Reads coverage in single base pair resolution using only 5-prime end of BAM file records. Coverages are reported for forward and reverse strands separately. Options for customized filtering of BAM records are provided.

Usage

read5endCoverage(bam, chroms = NULL, mapq = 30L, duplicate = FALSE,
  flag = scanBamFlag(isUnmappedQuery = FALSE, isSecondaryAlignment = FALSE,
  isNotPassingQualityControls = FALSE))

Arguments

bam	The path to a BAM file, which is sorted and indexed.
chroms	NULL or a vector of chromosome names that compatible with the provided BAM file. Reads coverage will be generated for these chromosomes. Default (NULL) will use all chromosomes in BAM file.
mapq	A non-negative integer specifying the minimum mapping quality to include. BAM records with mapping qualities less than mapq are discarded.
duplicate	A logical vector which, when FALSE (Default), returns maximum coverage of 1 for every base pair. Reads that start at the same position but on different strands are not treated as duplicates.
flag	A returned object by Rsamtools::scanBamFlag. Additional options for BAM records filtering.

Value

A list of two objects by GenomicRanges::coverage

fwd	Coverage object for forward strand.
rev	Coverage object for reverse strand.

Examples

bam <- system.file("extdata", "chipseq.bam", package="gcapc")
read5endCoverage(bam)

tengmx/gcapc documentation built on May 31, 2019, 8:35 a.m.