import.bam.ctss {CAGEr}R Documentation

import.bam.ctss

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


[Package CAGEr version 1.22.3 Index]