import.bam: import.bam

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

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"))

charles-plessy/CAGEr documentation built on Oct. 27, 2024, 10:11 p.m.