findPD: Find PRIMER DIMER reads.

In valenlab/amplican: Automated analysis of CRISPR experiments

Find PRIMER DIMER reads.

Description

Use to filter reads that are most likely PRIMER DIMERS.

Usage

findPD(aln, cfgT, PRIMER_DIMER = 30)

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.
PRIMER_DIMER	(numeric) Value specifying buffer for PRIMER DIMER detection. For a given read it will be recognized as PRIMER DIMER when alignment will introduce gap of size bigger than: length of amplicon - (lengths of PRIMERS + PRIMER_DIMER value)

Value

(logical) Where TRUE indicates event classified as PRIMER DIMER

See Also

findEOP findLQR

Other filters: findEOP(), findLQR()

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"))
findPD(aln, cfgT)

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