popdiv.convert {popgen}R Documentation

Convert a dataset for use in function popdif.

Description

Convert a matrix (in which the multi-locus genotypes of each individual are stored in 2 rows) to a format used by the function popdif.

Usage

popdiv.convert(x, miss = 0)

Arguments

x (2 * N, L + 1) matrix where N is the number of individuals and L is the number of loci. Each individual's genotypes are contained in 2 rows. The first entry of each specifies the individuals population. Each row has (L + 1) entries where L is the number of loci.
miss The code for missing values.

Value

List with components

NUMA Vector of the number of alleles at each loci
N LxP matrix containing the number of genotypes in each population at each locus.
X Matrix with L rows, one for each locus. Each row contains a list of allele counts from each population. For example, if there are 2 populations and the locus has 3 alleles then the first 3 entries in the row specify the allele counts in population 1 and the next 3 entries specify the allele counts in population 2. The rest of the row is set to 0.

Author(s)

Jonathan Marchini

See Also

popdiv

Examples


 ex <- read.table(paste(.libPaths(), "popgen", "example_data2", sep = .Platform$file.sep))
 X <- matrix(unlist(ex), nrow(ex), ncol(ex), byrow = FALSE)

 X1 <- popdiv.convert(X)


[Package popgen version 0.0-4 Index]