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 
[aut, cre],
John D. Storey
[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.pdf |
| Vignettes: |
Estimate Kinship and FST under Arbitrary Population Structure with 'popkin' |
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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