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 1.24.0 Index]