https://github.com/cran/ape
Tip revision: 042de1517b86bb884cd5eaeaeb488d9e59965f1f authored by Emmanuel Paradis on 01 February 2008, 00:00:00 UTC
version 2.1-1
version 2.1-1
Tip revision: 042de15
dist.gene.Rd
\name{dist.gene}
\alias{dist.gene}
\alias{dist.gene.pairwise}
\alias{dist.gene.percentage}
\title{Pairwise Distances from Genetic Data}
\usage{
dist.gene(x, method = "pairwise", variance = FALSE)
dist.gene.pairwise(x, variance = FALSE)
dist.gene.percentage(x, variance = FALSE)
}
\arguments{
\item{x}{a matrix or a data frame.}
\item{method}{a character string specifying the method used to compute
the distances; only two choices are available: \code{"pairwise"},
and \code{"percentage"}.}
\item{variance}{a logical, indicates whether the variance of the
distances should be returned (default to FALSE).}
}
\description{
These functions compute a matrix of distances between pairs of
individuals from a matrix or a data frame of genetic data.
}
\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 \eqn{d} between two
individuals is the number of loci for which they differ, and the
associated variance is \eqn{d(L - d)/L}, where \eqn{L} is the number
of loci.
In the case of the percentage method, this distance is divided by \eqn{L},
and the associated variance is \eqn{d(1 - d)/L}.
For more elaborate distances with DNA sequences, see the function
\code{dist.dna}.
}
\value{
either a numeric matrix with possibly the names of the individuals (as
given by the rownames of the argument \code{x}) as colnames and rownames
(if \code{variance = FALSE}, the default), or a list of two matrices names
\code{distances} and \code{variance}, respectively (if \code{variance =
TRUE}).
}
\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
\seealso{
\code{\link{dist.dna}}, \code{\link{cophenetic.phylo}}
}
\keyword{manip}