R: Prepare a primer table for downstream analyses

prepare_primer_df {prider} | R 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.

[Package prider version 1.0.4 Index]