designPrimers: Design primers

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

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)

• designPrimers(TsIO): Design primers using Primer3 from a TsIO object

• designPrimers(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)

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