extractEvents: Extract AlignmentsExperimentSet events into data.frame.
In valenlab/amplican: Automated analysis of CRISPR experiments

extractEvents

R Documentation

Extract AlignmentsExperimentSet events into data.frame.

Description

Extracts events (insertions, deletions, mismatches) from alignments into data.frame. Can use multiple cores as process is quite slow. All events are relative towards forward strand. "-" in strand column indicates which events were from reverse reads.

Usage

extractEvents(object, use_parallel = FALSE)

Arguments

`object`	(AlignmentsExperimentSet)
`use_parallel`	(boolean) Set to TRUE, if you have registered multicore back-end with `register`.

Value

(data.frame) Compatible with GRanges style.

Examples

file_path <- system.file("extdata", "results", "alignments",
                         "AlignmentsExperimentSet.rds", package = "amplican")
aln <- readRDS(file_path)
extractEvents(aln)

valenlab/amplican documentation built on Jan. 28, 2024, 5:10 a.m.