import.bam {CAGEr} | R Documentation

## import.bam

### Description

Imports CTSS data from a BAM file.

### Usage

    import.bam(
      filepath,
      filetype,
      sequencingQualityThreshold = 10,
      mappingQualityThreshold = 20
    )

### Arguments

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

### See Also

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

### Examples

    # TODO: add exmaple file
    # import.bam(system.file("extdata", "example.bam", package = "CAGEr"))

[Package CAGEr version 2.0.2 Index]