loadBam: Load a BAM file

In nzhang89/RiboSeeker: A Package for Ribosome Profiling Data Analysis and Visualization

Load a BAM file

Description

Load a BAM file. This function is essentially a wrapper of readGAlignments. Note that paried-end reads will be treated as single-end.

Usage

loadBam(
  bamFile,
  param = ScanBamParam(flag = scanBamFlag(isUnmappedQuery = FALSE, isSecondaryAlignment
    = FALSE, isNotPassingQualityControls = FALSE), mapqFilter = 0)
)

Arguments

bamFile	The path of a BAM file. Note that the BAM index file must also exist in the same folder and have the same prefix. For example, if the BAM file is aln.bam, then the BAM index file should be aln.bam.bai. (Required).
param	A ScanBamParam object. See Rsamtools package for more details. (Default: ScanBamParam(flag=scanBamFlag(isUnmappedQuery=FALSE, isSecondaryAlignment= FALSE, isNotPassingQualityControls=FALSE), mapqFilter=0)).

Value

A GAlignments object of the aligned reads.

nzhang89/RiboSeeker documentation built on April 15, 2022, 10:18 a.m.