GENESIS

DOI: 10.18129/B9.bioc.GENESIS    

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

Bioconductor version: Release (3.7)

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.

Author: Matthew P. Conomos, Stephanie M. Gogarten, Lisa Brown, Han Chen, Ken Rice, Tamar Sofer, Timothy Thornton, Chaoyu Yu

Maintainer: Stephanie M. Gogarten <sdmorris at uw.edu>

Citation (from within R, enter citation("GENESIS")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GENESIS")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GENESIS")

 

HTML R Script Genetic Association Testing using the GENESIS Package
HTML R Script Population Structure and Relatedness Inference using the GENESIS Package
PDF   Reference Manual
Text   NEWS

Details

biocViews BiocViews, DimensionReduction, GeneticVariability, Genetics, GenomeWideAssociation, PrincipalComponent, QualityControl, SNP, Software, StatisticalMethod
Version 2.10.0
In Bioconductor since BioC 3.1 (R-3.2) (3 years)
License GPL-3
Depends
Imports Biobase, BiocGenerics, GWASTools, gdsfmt, GenomicRanges, graph, IRanges, S4Vectors, SeqArray, SeqVarTools, dplyr, graphics, grDevices, Matrix, methods, stats, utils
LinkingTo
Suggests CompQuadForm, logistf, poibin, survey, SNPRelate, GWASdata, testthat, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GENESIS_2.10.0.tar.gz
Windows Binary GENESIS_2.10.0.zip
Mac OS X 10.11 (El Capitan) GENESIS_2.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GENESIS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GENESIS
Package Short Url http://bioconductor.org/packages/GENESIS/
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