DottedAlignment {QSutils} | R Documentation

## Align haplotypes into a dotted alignment

### Description

Given an alignment, it takes the first sequence as reference, and depicts all equivalences in the alignment as dots, leaving only the variants with respect to the reference.

### Usage

    DottedAlignment(hseqs)

### Arguments

`hseqs` | DNAStringSet or AAStringSet with haplotype sequences.

### Value

A character string vector of the alignment, with dots in the conserved positions.

### Author(s)

Mercedes Guerrero-Murillo and Josep Gregori

### See Also

`ReadAmplSeqs`

### Examples

    filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
    lst <- ReadAmplSeqs(filepath,type="DNA")
    strs <- DottedAlignment(lst$hseqs)

    # Create a data frame to visualize the result.
    data.frame(Hpl=strs,stringsAsFactors=FALSE)

[Package QSutils version 1.12.0 Index]