designPrimers {TAPseq} | R Documentation

## Design primers

### Description

Design primers based on `TsIO` or `TsIOList` objects. Creates boulder-IO records, passes input to Primer3 and parses the output.

### Usage

    designPrimers(
      object,
      thermo_params_path = NA,
      primer3_core = getOption("TAPseq.primer3_core")
    )

    ## S4 method for signature 'TsIO'
    designPrimers(
      object,
      thermo_params_path = NA,
      primer3_core = getOption("TAPseq.primer3_core")
    )

    ## S4 method for signature 'TsIOList'
    designPrimers(
      object,
      thermo_params_path = NA,
      primer3_core = getOption("TAPseq.primer3_core")
    )

### Arguments

`object` | `TsIO` or `TsIOList` object for which primers should be designed.
`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 new `TsIO` or `TsIOList` object containing Primer3 output.

### Methods (by class)

- `TsIO`: Design primers using Primer3 from a `TsIO` object

- `TsIOList`: Design primers using Primer3 from a `TsIOList` object

### See Also

http://primer3.org/manual.html for Primer3 manual and TsIO for TsIO class objects.

### Examples

    # chromosome 11 truncated transcript sequences and annotations
    data("chr11_truncated_txs_seq")

    # create TsIOList object for the first two sequence templates
    tapseq_io <- TAPseqInput(chr11_truncated_txs_seq[1:2], product_size_range = c(350, 500))

    # design primers
    ## Not run:
    tapseq_io <- designPrimers(tapseq_io)

    ## End(Not run)

    # designed primers are stored in the tapseq_primers slot
    tapseq_primers(tapseq_io)

[Package TAPseq version 0.99.6 Index]