generate_snp_search_string — generate_snp_search

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

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