queryPositions: Extract Variant Information for Specific Positions in an...

In HLAtools: Toolkit for HLA Immunogenomics

Extract Variant Information for Specific Positions in an Alignment

Description

Identifies the sequence variants at specific positions in specified alignments in HLAalignments. When 'table' is TRUE, data frames of counts and frequencies for each variant at each position are returned.

Usage

queryPositions(alignType, locus, positions, table = 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 locus supported by the IPD-IMGT/HLA Database.
positions	A vector of numeric variant positions.
table	A logical value specifying if a table of counts and frequencies for each variant at each value of 'positions' should be returned (table = TRUE). The default value is FALSE.

Value

When 'positions' specifies a single position, a character vector of variants is returned. When multiple positions are specified, a list of such character vectors is returned. When 'table' is TRUE, a list of data frames identifying the number (Count) and frequency (Frequency) of each variant is returned.

Note

This function requires that the HLAalignments object has been populated with alignments via the alignmentFull() function.

The '.' value in a vector of positions identifies absent sequence; e.g. following a nonsense mutation or in a region of sequence aligned to an insertion. The '*' value in a vector of positions identifies unknown sequence.

Examples

## Not run: 
queryPositions("prot","DRB1",c(5,10,86,129))
queryPositions("prot","DRB1",c(5,10,86,129),TRUE)

## End(Not run)

HLAtools documentation built on June 8, 2025, 12:24 p.m.