import.bam.ctss: import.bam.ctss

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

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()

charles-plessy/CAGEr documentation built on Nov. 4, 2023, 11:57 a.m.