getVariableAAPos {midasHLA} | R Documentation

## Find variable positions in sequence alignment

### Description

`getVariableAAPos` finds variable amino acid positions in protein sequence alignment.

### Usage

    getVariableAAPos(alignment, varchar = "[A-Z]")

### Arguments

`alignment` | Matrix containing amino acid level alignment, as returned by `readHlaAlignments`,
`varchar` | Regex matching characters that should be considered when looking for variable amino acid positions. See details for further explanations.

### Details

The variable amino acid positions in the alignment are those at which different amino acids can be found. As the alignments can also contain indels and unknown characters, the user choice might be to consider those positions as variable or not. This can be achieved by passing appropriate regular expression in `varchar`. Eg. when `varchar = "[A-Z]"` occurence of deletion/insertion (".") will not be treated as variability. In order to detect this kind of variability `varchar = "[A-Z\\.]"` should be used.

### Value

Integer vector specifying which alignment columns are variable.

### Examples

    alignment <- readHlaAlignments(gene = "TAP1")
    getVariableAAPos(alignment)

[Package midasHLA version 1.2.0 Index]