single_primer_design: Initiate the primer design for a single gene

In Acribbs/scAmpDesign:

Description

This function will design a primer set to use with targeted single-cell sequencing.

Usage

single_primer_design(
  ncbi = NULL,
  transcript_id_version = NULL,
  primer3 = NULL,
  thermo.param = system.file("extdata/primer3_config/", package = "scAmpDesign"),
  settings = system.file("extdata/primer3_settings.txt", package = "scAmpDesign"),
  ensembl_host = "http://uswest.ensembl.org/",
  dataset = "hsapiens_gene_ensembl"
)

Arguments

ncbi	An NBCI Reference. For example, the SARS-COV2 is NC_045512.
transcript_id_version	An Ensembl transcript id with version number. For example, the main transcript for FOXP3 is ENST00000376207.10.
primer3	The location of primer3_core. Example: primer3='/Users/adamcribbs/miniconda3/bin/primer3_core'
thermo.param	The location of the thermodynamic parameters folder. Currently within the R inst/extdata
settings	text file for parameters for primer 3. Currently within the inst/extdata
ensembl_host	Specify the host for ensembl. Defaults to "http://uswest.ensembl.org/".
ensembl_dataset	Specify the datasdets to be accessed by ensembl. Defaults to "hsapiens_gene_ensembl"

Value

A set of primer pairs

Examples

## Not run: 
single_primer_design(ncbi="NC_045512", primer3="/Users/adamcribbs/miniconda3/bin/primer3_core")
single_primer_design(transcript_id_version="ENST00000376207.10", primer3="/Users/adamcribbs/miniconda3/bin/primer3_core")

## End(Not run)

Acribbs/scAmpDesign documentation built on May 26, 2020, 9:56 p.m.