primer_qc: Perform a series of tests of a putative primer.

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

Perform a series of tests of a putative primer.

Description

This function should probably replace the morass of code found in snp_density_primers(). It is current used by snp_cds_primers().

Usage

primer_qc(
  entry,
  genome,
  variant_gr,
  target_temp = 60,
  direction = "fwd",
  run_pattern = "AAAA",
  min_gc_prop = 0.3,
  seq_object = NULL
)

Arguments

entry	Single row of the table of potential primers.
genome	bsgenome used to search against.
variant_gr	GRanges of variants to xref against.
target_temp	Desired Tm.
direction	Either fwd or rev.
run_pattern	Regex to look for bad runs of a single nt.
min_gc_prop	Minimum proportion of GC content.
seq_object	Used to hunt for multi-hit primers.

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