findPD {amplican} | R Documentation

## 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)

[Package amplican version 1.16.0 Index]