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 1.34.0 Index]