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 (3.19)
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("GENESIS")):
Installation
To install this package, start R (version "4.4") 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")| 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 | ||
| NEWS | Text |
Details
| biocViews | BiocViews, DimensionReduction, GeneticVariability, Genetics, GenomeWideAssociation, PrincipalComponent, QualityControl, SNP, Software, StatisticalMethod |
| Version | 2.34.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9.5 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.
| Source Package | GENESIS_2.34.0.tar.gz |
| Windows Binary (x86_64) | GENESIS_2.34.0.zip |
| macOS Binary (x86_64) | GENESIS_2.34.0.tgz |
| macOS Binary (arm64) | GENESIS_2.34.0.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 |