checkPrimers {TAPseq} | R Documentation

## Check primers for complementarity

### Description

Check a TAP-seq primer set, i.e. outer or inner primers for a target gene panel, for potential complementarity issues when multiplexing. Uses Primer3's `check_primers` functionality.

### Usage

    checkPrimers(
      object,
      primer_opt_tm = 63,
      primer_min_tm = 59,
      primer_max_tm = 66,
      thermo_params_path = NA,
      primer3_core = getOption("TAPseq.primer3_core")
    )

    ## S4 method for signature 'TsIO'
    checkPrimers(
      object,
      primer_opt_tm = 63,
      primer_min_tm = 59,
      primer_max_tm = 66,
      thermo_params_path = NA,
      primer3_core = getOption("TAPseq.primer3_core")
    )

    ## S4 method for signature 'TsIOList'
    checkPrimers(
      object,
      primer_opt_tm = 63,
      primer_min_tm = 59,
      primer_max_tm = 66,
      thermo_params_path = NA,
      primer3_core = getOption("TAPseq.primer3_core")
    )

### Arguments

`object` | A `TsIO` or `TsIOList` object containing designed primers.
`primer_opt_tm, primer_min_tm, primer_max_tm` | Optimal, minumum and maximum primer melting temperature. Should be the same values that were used when designing the primers.
`thermo_params_path` | Optional path (character) to the `primer3_config` directory. Only required when using Primer3 < 2.5.0.
`primer3_core` | Path (character) to the `primer3_core` executable. Usually this is inferred when loading/attaching the package.

### Value

A `data.frame` with `check_primers` results.

### Methods (by class)

- `TsIO`: Check primers from `TsIO` objects.

- `TsIOList`: Check primers from `TsIOList` objects.

### See Also

http://primer3.org/manual.html for Primer3 manual.

### Examples

    library(ggplot2)

    # chr11 primers example data
    data("chr11_primers")

    # pick best primers based on predicted off-targets for subset of all primers
    best_primers <- pickPrimers(chr11_primers, n = 1, by = "off_targets")

    # check for complementarity
    ## Not run:
    comp <- checkPrimers(best_primers)

    # plot complementarity scores for every pair. the lines indicate complementarity scores of 47,
    # the default value applied by Primer3 to identify high complementarity primer pairs
    ggplot(comp, aes(x = primer_pair_compl_any_th, y = primer_pair_compl_end_th)) +
      geom_hline(aes(yintercept = 47), colour = "darkgray", linetype = "dashed") +
      geom_vline(aes(xintercept = 47), colour = "darkgray", linetype = "dashed") +
      geom_point(alpha = 0.25) +
      theme_bw()

    ## End(Not run)

[Package TAPseq version 1.0.0 Index]