prepare_primer_df: Prepare a primer table for downstream analyses

View source: R/prider.R

prepare_primer_dfR Documentation

Prepare a primer table for downstream analyses

Description

Prepare a primer table for downstream analyses

Usage

prepare_primer_df(
  input_fasta,
  primer_length = 20,
  GCcheck = FALSE,
  GCmin = 0.4,
  GCmax = 0.6,
  GChalves = FALSE,
  GCsimilarity = 0.1
)

Arguments

input_fasta

A string. Name or filepath of the input FASTA file.

primer_length

A number. Sets the primer length. For applications involving two adjacent probes, the value should be set to two-fold the length of a single probe.

GCcheck

A logical. If TRUE, checks the GC contents of the primers and filters based on GCmin and GCmax.

GCmin

A decimal. If GCcheck is performed, this parameter determines the minimum proportional GC content.

GCmax

A decimal. If GCcheck is performed, this parameter determines the maximum proportional GC content.

GChalves

A logical. If TRUE, checks the GC contents separately for both halves of the primers and filters based on GCsimilarity. For example for applications involving two adjacent probes.

GCsimilarity

A number. If GChalves is performed, this parameter determines the maximum proportional GC content difference between the primer halves.

Value

A list containing sequence id conversions, primer matrix and a list of primers with their target sequences.


prider documentation built on March 18, 2022, 8 p.m.