import.bam.ctss: import.bam.ctss

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.ctss(filepath, filetype, sequencingQualityThreshold,
  mappingQualityThreshold, removeFirstG, correctSystematicG, genome)

Arguments

filepath	The path to the BAM file.
filetype	bam or bamPairedEnd.
sequencingQualityThreshold	See getCTSS().
mappingQualityThreshold	See getCTSS().
removeFirstG	See getCTSS().
correctSystematicG	See getCTSS().
genome	See coerceInBSgenome().

Value

Returns a CTSS object.

See Also

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

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