findEOP: Find Events Overlapping Primers.

In valenlab/amplican: Automated analysis of CRISPR experiments

Find Events Overlapping Primers.

Description

Very often alignments return deletions that are not real deletions, but rather artifact of incomplete reads eg.:

ACTGAAAAA------- <- this "deletion" should be filtered
ACTG----ACTGACTG

Usage

findEOP(aln, cfgT)

Arguments

aln	(data.frame) Should contain events from alignments in GRanges style with columns eg. seqnames, width, start, end.
cfgT	(data.frame) Needs columns Forward_Primer, ReversePrimer and Amplicon.

Value

(logical vector) where TRUE indicates events that are overlapping primers

See Also

findPD findLQR

Other filters: findLQR(), findPD()

Examples

file_path <- system.file("extdata", "results", "alignments",
                         "raw_events.csv", package = "amplican")
aln <- data.table::fread(file_path)
cfgT <- data.table::fread(
  system.file("extdata", "results", "config_summary.csv",
              package = "amplican"))
findEOP(aln, cfgT)

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