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 (2016) .


News

2017-09-11 - popkin 1.0.0.9000

  • Public release!

2017-11-21 - popkin 1.0.1.9000

  • Fix a bug in which genotypes input to popkin via a function (rather than a regular matrix or a BEDMatrix object) caused popkin to die. Now popkin behaves as expected. New test unit cases were added to test function inputs (previously this case was untested).

2017-11-24 - popkin 1.0.2.9000

  • Added option to set colors for the lines that separate subpopulations.

2018-01-08 - popkin 1.0.3

  • Minor non-code changes for first CRAN submission.

2018-01-13 - popkin 1.0.4

  • All doc examples are now run (all used to be "dontrun").

  • Other minor non-code changes for first CRAN submission.

2018-01-26 - popkin 1.0.5

  • Updated vignette code to work when suggested package "lfa" is not available (needed for CRAN tests). This change is not visible in rendered vignette included in package.

Reference manual

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install.packages("popkin")

1.0.5 by Alejandro Ochoa, a year ago


https://github.com/StoreyLab/popkin/


Report a bug at https://github.com/StoreyLab/popkin/issues


Browse source code at https://github.com/cran/popkin


Authors: Alejandro Ochoa [aut, cre] , John D. Storey [aut]


Documentation:   PDF Manual  


GPL-3 license


Imports Rcpp, RColorBrewer, graphics

Suggests BEDMatrix, testthat, knitr, rmarkdown, lfa

Linking to Rcpp, RcppEigen


Suggested by bnpsd.


See at CRAN