sequential_variants: Search a set of variants for ones which are relatively...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Search a set of variants for ones which are relatively sequential.

Description

One potential way to screen strains is to use PCR primers which should(not) anneal due to variants with respect to the genome. This function seeks to find variants which are clustered sufficiently close to each other that this is possible.

Usage

sequential_variants(
  snp_sets,
  conditions = NULL,
  minimum = 3,
  maximum_separation = 3,
  one_away_file = "one_away.csv",
  two_away_file = "two_away.csv",
  doubles_file = "doubles.csv",
  singles_file = "singles.csv"
)

Arguments

snp_sets	Result from get_snp_sets() containing the variants with respect to known conditions.
conditions	Set of conditions to search against.
minimum	Minimum number of variants required for a candiate.
maximum_separation	How far apart from each other are these >=minimum variants allowed to be?
one_away_file	Location to write variants that are no more than 1 base apart.
two_away_file	Location for those which are no more than 2 apart.
doubles_file	Write out variants which are 2 in a row.
singles_file	Write out the individual variants here.

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.