The GENESIS package provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides functions to perform PCAiR (Conomos et al., 2015, Gen Epi) and PCRelate (Conomos et al., 2016, AJHG). PCAiR performs a Principal Components Analysis on genomewide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. Unlike standard PCA, PCAiR accounts for relatedness in the sample to provide accurate ancestry inference that is not confounded by family structure. PCRelate uses ancestry representative principal components to adjust for population structure/ancestry and accurately estimate measures of recent genetic relatedness such as kinship coefficients, IBD sharing probabilities, and inbreeding coefficients. Additionally, functions are provided to perform efficient variance component estimation and mixed model association testing for both quantitative and binary phenotypes.
Package details 


Author  Matthew P. Conomos, Timothy Thornton, Stephanie M. Gogarten 
Bioconductor views  BiocViews DimensionReduction GeneticVariability Genetics GenomeWideAssociation PrincipalComponent QualityControl SNP StatisticalMethod 
Maintainer  Matthew P. Conomos <mconomos@uw.edu>, Stephanie M. Gogarten <sdmorris@u.washington.edu> 
License  GPL3 
Version  2.6.1 
Package repository  View on Bioconductor 
Installation 
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