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 (3.16)

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, Thomas Lumley, Kenneth Rice, Tamar Sofer, Adrienne Stilp, Timothy Thornton, Chaoyu Yu

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

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GENESIS")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("GENESIS")

 

HTML	R Script	Analyzing Sequence Data using the GENESIS Package
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	2.28.0
In Bioconductor since	BioC 3.1 (R-3.2) (8 years)
License	GPL-3
Depends
Imports	Biobase, BiocGenerics, BiocParallel, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils
LinkingTo
Suggests	CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene
SystemRequirements
Enhances
URL	https://github.com/UW-GAC/GENESIS
Depends On Me
Imports Me
Suggests Me	coxmeg
Links To Me
Build Report

Package Archives

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

Source Package	GENESIS_2.28.0.tar.gz
Windows Binary	GENESIS_2.28.0.zip (64-bit only)
macOS Binary (x86_64)	GENESIS_2.28.0.tgz
macOS Binary (arm64)	GENESIS_2.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GENESIS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GENESIS
Bioc Package Browser	https://code.bioconductor.org/browse/GENESIS/
Package Short Url	https://bioconductor.org/packages/GENESIS/
Package Downloads Report	Download Stats