getEvents {amplican} | R Documentation

## Transform aligned strings into GRanges representation of events.

### Description

Transforms aligned strings into GRanges representation with events of deletions, insertions and mismatches. Subject should come from one amplicon sequence, after alignment to many sequences (patterns).

### Usage

    getEvents(
      pattern,
      subject,
      scores,
      ID = "NA",
      ampl_shift = 1L,
      ampl_start = 1L,
      strand_info = "+"
    )

### Arguments

`pattern` | (character) Aligned pattern.
`subject` | (character) Aligned subject.
`scores` | (integer) Alignment scores of the pattern and subject.
`ID` | (character) Will be used as seqnames of output GRanges.
`ampl_shift` | (numeric) Possible shift of the amplicons.
`ampl_start` | (numeric) Real amplicon starts. `pairwiseAlignment` clips alignments, therefore to output GRanges relative to the amplicon sequence (subject) ranges have to be shifted.
`strand_info` | (character) Strands to assign.

### Value

(`GRanges`) Same as events.

[Package amplican version 1.16.0 Index]