chiCalc: A functions for the assessment of population genetic...

In kkeenan02/diveRsity-dev: Genetic diversity partition statistics and Informative locus selection using Fst, Gst, Dest(Jost Chao) G'st and In.

Description

chiCalc allows the calculation of locus $X^2$ as well as $X^2$ across loci and populations. P.values and significance indicators are also provided. The function accepts co-dominant genetic data in both 2 and 3 digit genepop formats.

Usage

chiCalc(infile = NULL, outfile = NULL, gp = 3, minFreq = NULL)

Arguments

infile	Specifying the name of the ‘genepop’(Rousset, 2008) file from which the statistics are to be calculated. This file can be in either the 3 digit of 2 digit format, and must contain only one whitespace separator (e.g. “space” or “tab”) between each column including the individual names column. The number of columns must be equal to the number of loci + 1 (the individual names column). If this file is not in the working directory the file path must be given. The name must be a character string (i.e. enclosed in “” or '').
outfile	Allows users to specify a prefix for an output folder. Name must a character string enclosed in either “” or ''.
gp	Specifies the digit format of the infile. Either 3 (default) or 2.
minFreq	This argument allows users to specify a minimum mean allele frequency, below which, allele classes should be excluded from the analysis. The chi-square test for heterogeneity works well for classes which are observed at least five times. As many alleles at microsatellite loci are not observed this frequently, this option allow for a more conservative assessment of population heterogeneity, only considering alleles equal to or above the specified frequency. minFreq can be single nominal frequency or a vector of frequencies.

Details

All results will be written to a user defined folder ("working_directory/outfile"), providing an argument is passed for 'outfile'. Results will be written to .txt files, and an R, object is also written to the current environment.

Value

chiTable

A character matrix of locus and overall $X^2$ values, as well as respective degrees of freedom, p.values and visual statistical significance.

Author(s)

Kevin Keenan <[e-mail]>

References

Rousset, F., “genepop'007: a complete re-implementation of the genepop software for Windows and Linux.,” Molecular ecology resources, vol. 8, no. 1, pp. 103-6, (2008).

Examples

# To run an example use the following format
#
# test_results <- chiCalc(infile = Test_data, outfile = 'out',
#                       gp = 3, minFreq = 0.05)

kkeenan02/diveRsity-dev documentation built on May 20, 2019, 10:46 a.m.