popkin: Estimate Kinship and FST under Arbitrary Population Structure

Provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index). Method described in Ochoa and Storey (2021) <doi:10.1371/journal.pgen.1009241>.

Version: 1.3.23
Depends: R (≥ 3.5.0)
Imports: RColorBrewer, graphics, grDevices, ape
Suggests: BEDMatrix, testthat, knitr, rmarkdown, bnpsd
Published: 2023-01-07
DOI: 10.32614/CRAN.package.popkin
Author: Alejandro Ochoa ORCID iD [aut, cre], John D. Storey ORCID iD [aut]
Maintainer: Alejandro Ochoa <alejandro.ochoa at duke.edu>
BugReports: https://github.com/StoreyLab/popkin/issues
License: GPL-3
URL: https://github.com/StoreyLab/popkin/
NeedsCompilation: no
Citation: popkin citation info
Materials: README, NEWS
CRAN checks: popkin results

Documentation:

Reference manual: popkin.html , popkin.pdf
Vignettes: Estimate Kinship and FST under Arbitrary Population Structure with 'popkin' (source, R code)

Downloads:

Package source: popkin_1.3.23.tar.gz
Windows binaries: r-devel: popkin_1.3.23.zip, r-release: popkin_1.3.23.zip, r-oldrel: popkin_1.3.23.zip
macOS binaries: r-release (arm64): popkin_1.3.23.tgz, r-oldrel (arm64): popkin_1.3.23.tgz, r-release (x86_64): popkin_1.3.23.tgz, r-oldrel (x86_64): popkin_1.3.23.tgz
Old sources: popkin archive

Reverse dependencies:

Reverse suggests: bnpsd, ggmix, simfam, simtrait

Linking:

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