GENESIS: GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
Version 2.8.0

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 PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a Principal Components Analysis on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. Unlike standard PCA, PC-AiR accounts for relatedness in the sample to provide accurate ancestry inference that is not confounded by family structure. PC-Relate 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

AuthorMatthew P. Conomos, Timothy Thornton, Stephanie M. Gogarten, Lisa Brown
Bioconductor views BiocViews DimensionReduction GeneticVariability Genetics GenomeWideAssociation PrincipalComponent QualityControl SNP StatisticalMethod
MaintainerMatthew P. Conomos <[email protected]>, Stephanie M. Gogarten <[email protected]>
LicenseGPL-3
Version2.8.0
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GENESIS")

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GENESIS documentation built on Nov. 17, 2017, 12:39 p.m.