loadFileIntoGPos {CAGEr} | R Documentation

## 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()`

[Package CAGEr version 2.0.2 Index]