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 1.24.0 Index]