import.bam.ctss {CAGEr} | R Documentation

## import.bam.ctss

### Description

Imports CTSS data from a BAM file.

### Usage

    import.bam.ctss(
      filepath,
      filetype,
      sequencingQualityThreshold,
      mappingQualityThreshold,
      removeFirstG,
      correctSystematicG,
      genome
    )

### Arguments

`filepath` | The path to the BAM file.
`filetype` | bam or bamPairedEnd.
`sequencingQualityThreshold` | See getCTSS().
`mappingQualityThreshold` | See getCTSS().
`removeFirstG` | See getCTSS().
`correctSystematicG` | See getCTSS().
`genome` | See coerceInBSgenome().

### Value

Returns a CTSS object.

### See Also

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

[Package CAGEr version 2.0.2 Index]