alleles2loci: Build Loci Object From Matrix of Alleles

In pegas: Population and Evolutionary Genetics Analysis System

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)

pegas documentation built on May 29, 2024, 2:27 a.m.