multiSearch {HLAtools}

Search Alignment Sequences at Multiple Positions for a Specified Allele

Description

Generates a character string of multiple protein, codon or nucleotide or genomic sequences at the specified positions for the specified allele name.

Usage

multiSearch(
  alignType,
  locus,
  allele,
  positions,
  prefix = TRUE,
  sep = "~",
  trimmed = FALSE
)

Arguments

alignType

The type of alignment being searched. Allowed values are "prot", codon", "nuc" and "gen". Only one 'alignType' value is allowed.

locus

A specific locus.

allele

An allele name.

positions

Nucleotide positions to search.

prefix

A logical that indicates if the position number(s) should be included in the result.

sep

Defines the separator between position sequences.

trimmed

A logical identifying whether 'allele' is a two-field, 'trimmed' allele name (trimmed=TRUE), or a full-length name (trimmed=FALSE). The default value is FALSE.

Value

codons (possibly with position number) at 'positions' for 'allele'. If 'allele' does not have a codon at 'position', ” will be returned.

Note

For internal HLAtools use only.