bigDivPart: Genetic differentiation statistics and their estimators for...

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

Description

bigDivPart allows for the calculation of four main diversity partition statistics and their respective estimators from large genepop files.

Usage

bigDivPart(infile = NULL, outfile = NULL,
           WC_Fst = FALSE, format = 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 ''.
WC_Fst	A Logical argument indicating whether Weir & Cockerham's 1984 F-statistics should be calculated.
format	A character string specifying the preferred output format for calculated results. The arguments txt or xlsx are valid when outfile is not NULL.

Details

All results are optionally written to a user defined directory in either .xlsx or .txt format. The function is identical to the divPart function without the pairwise or bootstrapping functionality.

Value

standard	A matrix containing identical data to the Standard_stats worksheet in the .xlsx workbook.
estimate	A matrix containing identical data to the Estimated_stats worksheet in the .xlsx workbook.

Author(s)

Kevin Keenan <[e-mail]>

References

Dragulescu, A.D., “xlsx: Read, write, formal Excel 2007 and Excel 97/2000/xp/2003 files”, R package version 0.4.2, url:http://CRAN.R-project.org/package=xlsx, (2012).

Guile, D.P., Shepherd, L.A., Sucheston, L., Bruno, A., and Manly, K.F., “sendplot: Tool for sending interactive plots with tool-tip content.”, R package version 3.8.10, url: http://CRAN.R-project.org/package=sendplot, (2012).

Hedrick, P., “A standardized genetic differentiation measure,” Evolution, vol. 59, no. 8, pp. 1633-1638, (2005).

Jost, L., “G ST and its relatives do not measure differentiation,” Molec- ular Ecology, vol. 17, no. 18, pp. 4015-4026, (2008).

Manly, F.J., “Randomization, bootstrap and Monte Carlo methods in biology”, Chapman and Hall, London, 1997.

Nei, M. and Chesser, R., “Estimation of fixation indices and gene diver- sities,” Ann. Hum. Genet, vol. 47, no. Pt 3, pp. 253-259, (1983).

R Development Core Team (2011). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/.

Revolution Analytics (2012). doParallel: Foreach parallel adaptor for the parallel package. R package version 1.0.1. http://CRAN.R-project.org/package=doParallel

Revolution Analytics (2012). foreach: Foreach looping construct for R. R package version 1.4.0. http://CRAN.R-project.org/package=foreach

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).

Weir, B.S. & Cockerham, C.C., Estimating F-Statistics, for the Analysis of Population Structure, Evolution, vol. 38, No. 6, pp. 1358-1370 (1984).

Examples

# simply use the following format to run the function
# 
# test_result <- bigDivPart(infile = 'mydata', outfile = "myresults',
#                           WC_Fst = TRUE, format = "txt")

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