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FinePop2 (version 0.4)

Fine-Scale Population Analysis (Rewrite for Gene-Trait-Environment Interaction Analysis)

Description

Statistical tool set for population genetics. The package provides following functions: 1) estimators of genetic differentiation (FST), 2) regression analysis of environmental effects on genetic differentiation using generalized least squares (GLS) method, 3) interfaces to read and manipulate 'GENEPOP' format data files). For more information, see Kitada, Nakamichi and Kishino (2020) .

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Install

install.packages('FinePop2')

Monthly Downloads

169

Version

0.4

License

GPL (>= 2.0)

Maintainer

Reiichiro Nakamichi

Last Published

February 28th, 2020

Functions in FinePop2 (0.4)

GLS

Generalized least squres for regression analysis considering auto correlation.
locus_specificFST

Locus-specific global FST (Kitada et al. 2007, 2017).
herring

An example dataset of Atlantic herring.
clip.GENEPOP

Remove designated markers from a GENEPOP file.
pop_pairwiseFST

Genome-wide poppulation-paiwise FST (Nei & Chesser 1983).
pop_specificFST

Genome-wide population-specific FST (Weir & Goudet 2017).
globalFST

Genome-wide global FST (Weir & Cockerham 1984).
read.GENEPOP

Create a genotype data object of populations from a GENEPOP format file.
FinePop2-package

FinePop2
jsmackerel

An example dataset of Japanese Spanich mackerel in GENEPOP and frequency format.