findEOP: Find Events Overlapping Primers.
In amplican: Automated analysis of CRISPR experiments

Description Usage Arguments Value See Also Examples

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

1 2	ACTGAAAAA------- <- this "deletion" should be filtered ACTG----ACTGACTG

1	findEOP(aln, cfgT)

`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.

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

findPD findLQR

Other filters: findLQR, findPD

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)