R: Build Loci Object From Matrix of Alleles

alleles2loci {pegas} | R Documentation

## Build Loci Object From Matrix of Alleles

### Description

These functions transform a matrix of alleles into an object of class `"loci"`, or the reverse operation.

### Usage

    alleles2loci(x, ploidy = 2, rownames = NULL, population = NULL,
                 phased = FALSE)
    loci2alleles(x)

### Arguments

`x` | a matrix or a data frame where each column is an allele, or an object of class `"loci"`.
`ploidy` | an integer specifying the level of ploidy.
`rownames` | an integer giving the column number to be used as rownames of the output.
`population` | an integer giving the column number to be used as population (if any).
`phased` | a logical specifying whether the genotypes should be output as phased. By default, they are unphased.

### Details

Genetic data matrices are often arranged with one allele in each column of the matrix (particularly for micro-satellites), so that the number of columns is equal to the number of loci times the level of ploidy. `alleles2loci` transforms such matrices into a `"loci"` object.

If the rownames of the input matrix are already set, they are used in the output. Alternatively, it is possible to specify which column to use as rownames (this column will be deleted before creating the genotypes).

If the input matrix has colnames, then the names of the first column of each genotype is used as names of the output loci (see examples).

`loci2alleles` checks that all individuals have the ploidy for a given locus (if not an error occurs), but ploidy can vary among loci.

### Value

an object of class `"loci"` or a matrix.

### Author(s)

Emmanuel Paradis

### See Also

`read.loci`, `as.loci`

The vignette “ReadingFiles” explains how to read such a data set from Dryad (https://datadryad.org/stash).

### Examples

    x <- matrix(c("A", "A", "A", "a"), 2)
    colnames(x) <- c("Loc1", NA)
    y <- alleles2loci(x)
    print(y, details = TRUE)
    loci2alleles(y)

[Package pegas version 1.1 Index]