dist.gene

From ape v2.1-1
0th

Percentile

Pairwise Distances from Genetic Data

These functions compute a matrix of distances between pairs of individuals from a matrix or a data frame of genetic data.

Keywords
manip
Usage
dist.gene(x, method = "pairwise", variance = FALSE)
dist.gene.pairwise(x, variance = FALSE)
dist.gene.percentage(x, variance = FALSE)
Arguments
x
a matrix or a data frame.
method
a character string specifying the method used to compute the distances; only two choices are available: "pairwise", and "percentage".
variance
a logical, indicates whether the variance of the distances should be returned (default to FALSE).
Details

This function is meant to be very general and accepts different kinds of data (alleles, haplotypes, DNA sequences, and so on). The rows of the data matrix represent the individuals, and the columns the loci.

In the case of the pairwise method, the distance $d$ between two individuals is the number of loci for which they differ, and the associated variance is $d(L - d)/L$, where $L$ is the number of loci.

In the case of the percentage method, this distance is divided by $L$, and the associated variance is $d(1 - d)/L$.

For more elaborate distances with DNA sequences, see the function dist.dna.

Value

• either a numeric matrix with possibly the names of the individuals (as given by the rownames of the argument x) as colnames and rownames (if variance = FALSE, the default), or a list of two matrices names distances and variance, respectively (if variance = TRUE).

dist.dna, cophenetic.phylo