createIORecord: Create boulder IO record

In argschwind/TAPseq: Targeted scRNA-seq primer design for TAP-seq

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)

• createIORecord(TsIO): Create IO record from TsIO objects.

• createIORecord(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)

argschwind/TAPseq documentation built on Feb. 9, 2024, 8:20 p.m.