extractEvents: Extract AlignmentsExperimentSet events into data.frame.

In amplican: Automated analysis of CRISPR experiments

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)

amplican documentation built on Nov. 8, 2020, 11:10 p.m.