import.bam {CAGEr}R Documentation

import.bam

Description

Imports CTSS data from a BAM file.

Usage

import.bam(filepath, filetype, sequencingQualityThreshold = 10,
  mappingQualityThreshold = 20)

Arguments

filepath

The path to the BAM file.

filetype

bam or bamPairedEnd.

sequencingQualityThreshold

See getCTSS().

mappingQualityThreshold

See getCTSS().

See Also

Other loadFileIntoGPos: bam2CTSS, import.CTSS, import.bam.ctss, import.bedCTSS, import.bedScore, import.bedmolecule, loadFileIntoGPos, moleculesGR2CTSS

Examples

# TODO: add exmaple file
# import.bam(system.file("extdata", "example.bam", package = "CAGEr"))

[Package CAGEr version 1.22.3 Index]