addClipped {CrispRVariants} | R Documentation

## Extrapolates mapping location from clipped, aligned reads

### Description

Extrapolates the mapping location of a read by assuming that the clipped regions should map adjacent to the mapped locations. This is not always a good assumption, particularly in the case of chimeric reads!

### Usage

    addClipped(bam, ...)

    ## S4 method for signature 'GAlignments'
    addClipped(bam, ...)

### Arguments

`bam` | A GAlignments object
`...` | additional arguments

### Value

A `GRanges` representation of the extended mapping locations

### Author(s)

Helen Lindsay

[Package CrispRVariants version 1.8.0 Index]