import.bam: import.bam

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

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"))

CAGEr documentation built on Jan. 17, 2021, 2 a.m.