findEOP {amplican} | R Documentation |
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
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
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)