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Bioconductor - GENESIS (development version)

GENESIS

This is the development version of GENESIS; for the stable release version, see 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: Development (3.22)

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>

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

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
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 HTML R Script Reference Manual PDF NEWS Text Details biocViews BiocViews, DimensionReduction, GeneticVariability, Genetics, GenomeWideAssociation, PrincipalComponent, QualityControl, SNP, Software, StatisticalMethod Version 2.39.1 In Bioconductor since BioC 3.1 (R-3.2) (10 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 System Requirements URL https://github.com/UW-GAC/GENESIS See More Suggests CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene Linking To Enhances Depends On Me RAIDS Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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