findEOP {amplican} | R Documentation

## 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)

[Package amplican version 1.8.2 Index]