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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GENESIS")
In most cases, you don't need to download the package archive at all.
GENESIS
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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 (3.4)
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 and Timothy Thornton
Maintainer: Matthew P. Conomos <mconomos 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
| HTML | R Script | Genetic Association Testing using the GENESIS Package |
| HTML | R Script | Population Structure and Relatedness Inference using the GENESIS Package |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | BiocViews, DimensionReduction, GeneticVariability, Genetics, GenomeWideAssociation, PrincipalComponent, QualityControl, SNP, Software, StatisticalMethod |
| Version | 2.4.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (2 years) |
| License | GPL-3 |
| Depends | |
| Imports | GWASTools, SeqArray, SeqVarTools, Biobase, gdsfmt, graph, grDevices, graphics, stats, utils |
| LinkingTo | |
| Suggests | SNPRelate, logistf, survey, CompQuadForm, RUnit, BiocGenerics, 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.
| Package Source | GENESIS_2.4.0.tar.gz |
| Windows Binary | GENESIS_2.4.0.zip |
| Mac OS X 10.9 (Mavericks) | GENESIS_2.4.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/GENESIS/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/GENESIS/ |
| Package Downloads Report | Download Stats |
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