choose_sequence_regions: Given a named vector of fun regions, make a dataframe which...

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

Given a named vector of fun regions, make a dataframe which includes putative primers and the spec strings for expected variants.

Description

This function came out of our TMRC2 work and seeks to provide an initial set of potential PCR primers which are able to distinguish between different aspects of the data. In the actual data, we were looking for differences between the zymodemes 2.2 and 2.3.

Usage

choose_sequence_regions(
  long_variant_vector,
  max_primer_length = 45,
  topn = NULL,
  bin_width = 600,
  genome = NULL,
  target_temp = 58,
  min_gc_prop = 0.25,
  max_nmer_run = 5
)

Arguments

long_variant_vector	variant-based set of putative regions with variants between conditions of interest.
max_primer_length	given this length as a start, whittle down to a hopefully usable primer size.
topn	Choose this number of variant regions from the rather larger set of possibilities..
bin_width	Separate the genome into chunks of this size when hunting for primers, this size will therefore be the approximate PCR amplicon length.
genome	(BS)Genome to search.
target_temp	PCR temperature to attempt to match.
min_gc_prop	Cutoff for minimum required GC content.
max_nmer_run	Maximum run of the same nucleotide allowed.

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