rmMultiPCRChimera {CrispRVariants} | R Documentation

## Remove chimeric reads overlapping multiple primers

### Description

Finds and removes sets of chimeric read alignments that overlap more than one guide, i.e. that cannot be unambiguously assigned to a single guide.

### Usage

    rmMultiPCRChimera(readnames, pcrhits, chimera_idxs, ...)

    ## S4 method for signature 'character,Hits,integer'
    rmMultiPCRChimera(readnames, pcrhits,
      chimera_idxs, ..., verbose = TRUE)

### Arguments

`readnames` | A set of read names, used for identifying chimeric read sets
`pcrhits` | A mapping between indices of reads and a set of pcr primers
`chimera_idxs` | location of chimeric reads within the bam
`...` | Additional arguments
`verbose` | Display information about the chimeras (Default: TRUE)

### Value

pcrhits, with chimeric reads mapping to different primers omitted.

### Author(s)

Helen Lindsay

[Package CrispRVariants version 1.12.0 Index]