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 2.0.1 Index]