amplicanOverlap: Check which events overlap expected cut sites.

In valenlab/amplican: Automated analysis of CRISPR experiments

Check which events overlap expected cut sites.

Description

To determine which deletions, insertions and mismatches (events) are probably created by CRISPR we check whether they overlap expected cut sites. Expected cut sites should be specified in UPPER CASE letters in the amplicon sequences.

Usage

amplicanOverlap(aln, cfgT, cut_buffer = 5, relative = FALSE)

Arguments

aln	(data.frame) Contains relevant events in GRanges style.
cfgT	(data.frame) Contains amplicon sequences.
cut_buffer	(numeric) Number of bases that should expand 5' and 3' of the specified expected cut sites.
relative	(boolean) Sets whether events are relative to the position of the target site.

Value

(bolean vector) Where TRUE means that given event overlaps cut site.

See Also

Other analysis steps: amplicanAlign(), amplicanConsensus(), amplicanFilter(), amplicanMap(), amplicanNormalize(), amplicanPipelineConservative(), amplicanPipeline(), amplicanReport(), amplicanSummarize()

Examples

file_path <- system.file("test_data", "test_aln.csv", package = "amplican")
aln <- data.table::fread(file_path)
cfgT <- data.table::fread(
  system.file("test_data", "test_cfg.csv", package = "amplican"))
all(aln$overlaps == amplicanOverlap(aln, cfgT))

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