multiSearch {HLAtools} | R Documentation |
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.