read.fstat: Reads data from a FSTAT file

Description Usage Arguments Value References Examples

Description

Imports a FSTAT data file into R. The data frame created is made of nl+1 columns, nl being the number of loci. The first column corresponds to the Population identifier, the following columns contains the genotypes of the individuals.

Usage

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read.fstat(fname, na.s = c("0","00","000","0000","00000","000000","NA"))

Arguments

fname

a file in the FSTAT format (http://www.unil.ch/popgen/softwares/fstat.htm): The file must have the following format:

The first line contains 4 numbers: the number of samples, np , the number of loci, nl, the highest number used to label an allele, nu, and a 1 if the code for alleles is a one digit number (1-9), a 2 if code for alleles is a 2 digit number (01-99) or a 3 if code for alleles is a 3 digit number (001-999). These 4 numbers need to be separated by any number of spaces.

The first line is immediately followed by nl lines, each containing the name of a locus, in the order they will appear in the rest of the file.

On line nl+2, a series of numbers as follow:

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1     0102   0103   0101  0203          0      0303

The first number identifies the sample to which the individual belongs, the second is the genotype of the individual at the first locus, coded with a 2 digits number for each allele, the third is the genotype at the second locus, until locus nl is entered (in the example above, nl=6). Missing genotypes are encoded with 0, 00, 0000, 000000 or NA. Note that 0001 or 0100 are not a valid format, as both alleles at a locus have to be known, otherwise, the genotype is considered as missing. No empty lines are needed between samples.

na.s

The strings that correspond to the missing value. You should note have to change this

Value

a data frame containing the desired data, in a format adequate to pass to varcomp

References

Goudet J. (1995). FSTAT (Version 1.2): A computer program to calculate F- statistics. Journal of Heredity 86:485-486

Goudet J. (2005). Hierfstat, a package for R to compute and test variance components and F-statistics. Molecular Ecology Notes. 5:184-186

Examples

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read.fstat(paste(path.package("hierfstat"),"/extdata/diploid.dat",sep="",collapse=""))

hierfstat documentation built on Nov. 17, 2021, 5:08 p.m.