loadFileIntoGPos: loadFileIntoGPos

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

loadFileIntoGPos

Description

A private (non-exported) function to load from each file format supported by CAGEr

Usage

loadFileIntoGPos(
  filepath,
  filetype = c("bam", "bamPairedEnd", "bed", "bedctss", "bedScore", "CAGEscanMolecule",
    "ctss"),
  sequencingQualityThreshold,
  mappingQualityThreshold,
  removeFirstG,
  correctSystematicG,
  genome
)

Arguments

filepath	The path to the file to load.
filetype	The type of the file
sequencingQualityThreshold	See getCTSS().
mappingQualityThreshold	See getCTSS().
removeFirstG	See getCTSS().
correctSystematicG	See getCTSS().
genome	See coerceInBSgenome().

Value

A GPos() object where the score represents the number of CAGE tags starting on that nucleotide.

See Also

import.CTSS

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

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