Demerelate (version 0.8-1)

Demerelate-package: Demerelate --- Algorithms to estimate pairwise relatedness within populations based on allele sharing

Description

The package Demerelate provides several functions to calculate relatedness of individuals based on diploid genetic markers. Following indices can be calculated:

1. $B_{xy}$(number of alleles shared) as described in Li and Horvitz 1953.
2. $M_{xy}$(genotype sharing) as described in Blouin et al. 1996. Sharing rate is calculated according to shared allele positions i.e. 0, 1 or 2 shared allele postions for diploids. A sharing rate of 0 is calculated if no alleles are shared, a rate of 0.5 if one allele position is equal in individuals and a rate of 1 if individuals match in both allele positions.
3. The estimator$r_{xy}$based on Queller and Goodnight 1989 adapted to pairwise comparisons as described in Oliehoek et al. 2006 is calculated as follows:ll{ $r_{xy,l} = \frac{0.5(I_{ac}+I_{ad}+I_{bc}+I_{bd})-p_{a}-p_{b}}{1+I_{ab}-p_{a}-p_{b}}$ $I_{a-d} =$allele identities of individual I in locus l $p_{a-b} =$frequencies of allele a or b in reference populations

eqn

$F_{is}$

Details

ll{ Package: Demerelate Version: 0.8-1 Date: 2013-12-17 Depends: R (>= 2.15.0), Formula Imports: fts, mlogit, sfsmisc, vegan Suggests: MASS License: GPL (>= 2) URL: http://www.r-project.org }

ll{ Demerelate -- Head function to calculate pairwise relatedness Loci.test -- Function to analyse datasets of diploid genetic information F.stat -- Function to calculate $F_{is}$ values for single populations demerelpop -- Example data set from randomized diploid markers for three populations demerelref -- Example data set from randomized diploid markers as reference demereldist -- Example data set from randomized relative geographic information }

References

Armstrong, W. (2012) fts: R interface to tslib (a time series library in c++). by R package version 0.7.7. Blouin, M.S. et al. (1996) Use of microsatellite loci to classify individuals by relatedness. Molecular Ecology, 5, 393-401. Croissant, Y. 2011 mlogit: multinomial logit model. R package version 0.2-2. Li C.C. and Horvitz D.G. (1953) Some methods of estimating the inbreeding coefficient. American Journal of Human Genetics 5, 107-17. Maechler, M. and myn others. (2012) Utilities from Seminar fuer Statistik ETH Zurich. R package version 1.0-20. Nei, M. (1977) F-statistics and analysis of gene diversity in subdivided populations. Annals of Human Genetics, 41, 225-233. Nei, M. and Chesser R.K. (1983) Estimation of fixation indices and gene diversities. Annals of Human Genetics, 47, 253-259. Oliehoek, P. A. et al. (2006) Estimating relatedness between individuals in general populations with a focus on their use in conservation programs. Genetics, 173, 483-496. Oksanen, J. et al. (2013) vegan: Community Ecology Package. R package version 2.0-8. Queller, D.C. and Goodnight, K.F. (1989) Estimating relatedness using genetic markers. Evolution, 43, 258-275. Weir, B.S. and Cockerham, C.C. (1984) Estimating F-Statistics for the analysis of population structure. Evolution, 38, 1358-1370.