loadFileIntoGPos: loadFileIntoGPos

Description Usage Arguments Value See Also

View source: R/ImportMethods.R

Description

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

Usage

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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


CAGEr documentation built on Jan. 17, 2021, 2 a.m.