prider: Prider

In manutamminen/prider: Multiplexed Primer Design by Linear Set Coverage Approximation

Prider

Description

Prepare a nearly optimal primer coverage for an input FASTA file.

Usage

prider(
  fasta_file,
  primer_length = 20,
  minimum_primer_group_size = 10,
  minimum_seq_group_size = 2,
  cum_cov_decimals = 2,
  NTkeep = "basic",
  GCcheck = FALSE,
  GCmin = 0.4,
  GCmax = 0.6,
  GChalves = FALSE,
  GCsimilarity = 0.1
)

## S3 method for class 'prider'
print(x, ...)

## S3 method for class 'prider'
plot(x, ...)

Arguments

fasta_file	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.
minimum_primer_group_size	A number. Sets the minimum number of primers per primer cluster; smaller primer clusters will be discarded.
minimum_seq_group_size	A number. Sets the minimum number of sequences each primer cluster has to cover.
cum_cov_decimals	A number. Sets the number of decimals for cumulative coverage of primer clusters. Generally, lower value corresponds to less clusters and higher value to more clusters in the output. If the clusters do not cover the input sequences sufficiently, increasing this value may increase the coverage. If the clusters overlap too much, lowering the value may reduce this effect. Recommended range 1-4.
NTkeep	A string. Filters the primers based on the nucleotides. "basic" = keeps only the primers with G, C, T or A. "N" = keeps primers with G, C, T, A and N. "any" = keeps primers with the IUPAC nucleotide code characters. "all" = keeps all primers.
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. Used for example for applications involving two adjacent probes.
GCsimilarity	A decimal. If GChalves is performed, this parameter determines the maximum proportional GC content difference between the primer halves.
x	An object from prider function.
...	Other arguments.

Value

A list containing a sequence conversion table, primer candidates table, excluded sequences table and a primer coverage table.

Author(s)

Manu Tamminen <[e-mail]>, Niina Smolander <[e-mail]>

Examples

test_fasta <- system.file('extdata', 'test.fasta', package = 'prider')

# Runs Prider with the default values:
primer_designs <- prider(test_fasta)

# Returns all the primers:
primers(primer_designs)
# Returns the primers of a specific primer group:
primers(primer_designs)[1]
# Returns all the sequences:
sequences(primer_designs)
# Returns the sequence of a specific Id:
sequences(primer_designs)[1]
# Plots the primers groups and the target sequences as a heatmap:
plot(primer_designs)

manutamminen/prider documentation built on July 30, 2022, 3:17 a.m.