generate_snp_search_string {minSNPs}

generate_snp_search_string

Description

generate_snp_search_string identify the SNPs that will overlap the search strings generated from the targeted SNPs

Usage

generate_snp_search_string(
  selected_snps,
  position_reference,
  ref_seq,
  snp_matrix,
  prev,
  after,
  position_type = "fasta",
  extend_length = TRUE,
  fasta_name_as_result = TRUE,
  bp = MulticoreParam()
)

Arguments

selected_snps

list of targeted SNPs

position_reference

the mapping between reference genome positions and orthologous SNP matrix positions

ref_seq

the reference genome sequence

snp_matrix

the orthologous SNP matrix

prev

number of characters before the SNP

after

number of characters after the SNP

position_type

type of SNPs input, "fasta" (orthologous SNP matrix based) or "genome" (reference genome based); Default to "fasta"

extend_length

whether to extend the search string before and after the SNP and ignore overlapping SNPs

fasta_name_as_result

Whether the result should use the fasta matching sequence name or the fasta position and allele, default to using fasta sequence name (TRUE)

bp

BiocParallel backend to use

Value

a dataframe containing the search strings