pickPrimers {TAPseq} | R Documentation

## Pick best TAP-seq primers

### Description

Pick based primers from designed primers for every target based on Primer3 penalty score or off-target priming estimated with `blastPrimers`.

### Usage

    pickPrimers(object, n = 1, by = c("penalty", "off_targets"))

    ## S4 method for signature 'TsIO'
    pickPrimers(object, n = 1, by = c("penalty", "off_targets"))

    ## S4 method for signature 'TsIOList'
    pickPrimers(object, n = 1, by = c("penalty", "off_targets"))

### Arguments

`object` | A `TsIO` or `TsIOList` object containing designed primers.
`n` | The number of top primers to pick (default: 1, which returns the best primer).
`by` | Attribute by which primers should be picked. Can be either `penalty` or `off_targets`.

### Details

If `by` is set to `off_targets` top primers are picked based on the lowest number of exonic, intronic and intergenic off-targets (in that priority).

### Value

A `TsIO` or `TsIOList` object containing the picked primers.

### Methods (by class)

- `TsIO`: Pick best primers in a `TsIO` object

- `TsIOList`: Pick best primers per target in a `TsIOList` object

### Examples

    # chr11 primers examples
    data("chr11_primers")

    # pick the best primer per gene based on the fewest exonic, intronic and intergenic off-targets
    # (in that order)
    best_primers <- pickPrimers(chr11_primers, by = "off_targets")
    tapseq_primers(best_primers)

    # pick the best two primers per gene based on the lowest penalty score computed by Primer3
    best_primers <- pickPrimers(chr11_primers, n = 2, by = "penalty")
    tapseq_primers(best_primers)

[Package TAPseq version 1.4.0 Index]