createIORecord {TAPseq} | R Documentation

## Create boulder IO record

### Description

Takes a `TsIO` or `TsIOList` object and converts it into a boulder IO record for Primer3. Essentially it converts it into a list of character vectors that each contain the tag and the value in the form: "TAG=VALUE". More on this format can be found in the Primer3 manual.

### Usage

    createIORecord(object, thermo_params_path = NA)

    ## S4 method for signature 'TsIO'
    createIORecord(object, thermo_params_path = NA)

    ## S4 method for signature 'TsIOList'
    createIORecord(object, thermo_params_path = NA)

### Arguments

`object` | TsIO of TsIOList object for which a Primer3 boulder IO record should be created.
`thermo_params_path` | Optional path (character) to the `primer3_config` directory. Only required when using Primer3 < 2.5.0.

### Details

This function is usually not needed by the user, because functions such as `designPrimers` handle IO record generation. However, this function can for instance be useful to generate IO records, write them to a file and pass them to Primer3 in the conventional way.

### Value

A character vector containing the lines of the IO record.

### Methods (by class)

- `TsIO`: Create IO record from `TsIO` objects.

- `TsIOList`: Create IO record from `TsIO` objects.

### See Also

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

### Examples

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

    # create TsIOList object for primer desing from sequence templates
    obj <- TAPseqInput(chr11_truncated_txs_seq, product_size_range = c(350, 500))

    # create boulder IO record
    boulder_io <- createIORecord(obj)
    head(boulder_io, 11)

[Package TAPseq version 0.99.6 Index]