snp_cds_primers: Look for variants associated with CDS regions instead of...
In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

snp_cds_primers

R Documentation

Look for variants associated with CDS regions instead of high-density.

Description

The function snp_density_primers looks for regions with many variants. This flips the script and looks first to the set of CDS regions. It also makes heavy use of GRanges and so should prove useful as a reference when looking for range examples.

Usage

snp_cds_primers(
  cds_gr,
  variant_gr,
  bsgenome,
  amplicon_size = 600,
  min_overlap = 200,
  minvar_perbin = 10,
  super_len = 30,
  target_temp = 60,
  min_gc_prop = 0.3,
  max_nmer_run = 4,
  count_occurrences = TRUE,
  occurrence_mismatch = 0
)

Arguments

`cds_gr`	GRanges of CDS features. It does not have to be CDS, but probably should not be genes.
`variant_gr`	GRanges of observed variants. I get this by coercing my peculiar variant rownames into a GR.
`bsgenome`	Genome containing all the contigs mentioned above.
`amplicon_size`	Desired PCR amplicon for sequencing.
`min_overlap`	Desired overlap between every genome bin and CDS. Note I didn't say amplicon here because of the way I am making the primers.
`minvar_perbin`	Discard bins with less than this number of variants inside them.
`super_len`	I start out with a 'superprimer' which is assumed to be longer than needed for the target Tm. It is this long.
`target_temp`	Attempt to create primers with this Tm.
`min_gc_prop`	Warn or discard primers with less than this GC content.
`max_nmer_run`	Warn or discard primers with runs of a single base this long.
`count_occurrences`	Count up how many times the primer is found in the genome, hopefully this is always 1. Annoyingly, the vcountDict function does not allow mismatches.
`occurrence_mismatch`	I cannot use this, but I want to.