GENESIS: GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
Version 2.6.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorMatthew P. Conomos, Timothy Thornton, Stephanie M. Gogarten
Bioconductor views BiocViews DimensionReduction GeneticVariability Genetics GenomeWideAssociation PrincipalComponent QualityControl SNP StatisticalMethod
Date of publicationNone
MaintainerMatthew P. Conomos <mconomos@uw.edu>, Stephanie M. Gogarten <sdmorris@u.washington.edu>
LicenseGPL-3
Version2.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GENESIS")

Man pages

admixMapMM: admixMapMM
assocTestMM: SNP Genotype Association Testing with Mixed Models
assocTestSeq: Aggregate Association Testing with Sequencing Data
assocTestSeqWindow: Aggregate Association Testing with Sequencing Data in Sliding...
fitNullMM: Fit a Mixed Model Under the Null Hypothesis
fitNullReg: Fit a Regression Model Under the Null Hypothesis
GENESIS-package: GENetic EStimation and Inference in Structured samples...
HapMap_ASW_MXL_KINGmat: Matrix of Pairwise Kinship Coefficient Estimates for the...
king2mat: Convert KING text output to an R Matrix
pcair: PC-AiR: Principal Components Analysis in Related Samples
pcairPartition: Partition a sample into an ancestry representative 'unrelated...
pcrelate: PC-Relate: Model-Free Estimation of Recent Genetic...
pcrelateMakeGRM: Creates a Genetic Relationship Matrix (GRM) of Pairwise...
pcrelateReadInbreed: Create a Table of Inbreeding Coefficient Estimates from...
pcrelateReadKinship: Create a Table of Pairwise Kinship Coefficient and IBD...
plot.pcair: PC-AiR: Plotting PCs
varCompCI: Variance Component Confidence Intervals

Functions

GENESIS Man page
GENESIS-package Man page
HapMap_ASW_MXL_KINGmat Man page
XchromCode Source code
YchromCode Source code
admixMapMM Man page Source code
alleleFreq Source code
assocTestMM Man page Source code
assocTestSeq Man page Source code
assocTestSeqWindow Man page Source code
calculateProjection Source code
chrToInt Source code
createDesignMatrix Source code
estISAF Source code
fitNullMM Man page Source code
fitNullReg Man page Source code
getBlocks Source code
getScanIndex Source code
getSnpIndex Source code
getVariantInclude Source code
hasSex Source code
integrateFxn Source code
king2mat Man page Source code
ntToChr Source code
outputColumns Source code
paramChecks Source code
pcair Man page Source code
pcairPartition Man page Source code
pcrelate Man page Source code
pcrelateMakeGRM Man page Source code
pcrelateReadInbreed Man page Source code
pcrelateReadKinship Man page Source code
plot.pcair Man page Source code
prepareGenotype Source code
print.pcair Man page Source code
print.summary.pcair Man page Source code
runAIREMLgaussian Source code
runAIREMLother Source code
runBurdenTest Source code
runSKATTest Source code
skatO_qchisqsum Source code
skewness Source code
subsetCholSigmaInv Source code
summary.pcair Man page Source code
varCompCI Man page Source code
weightFromFreq Source code

Files

DESCRIPTION
NAMESPACE
R
R/SeqVarData_utils.R
R/admixMapMM.R
R/alleleFreq.R
R/assocTestMM.R
R/assocTestSeq.R
R/createDesignMatrix.R
R/estISAF.R
R/fitNullMM.R
R/fitNullReg.R
R/getBlocks.R
R/getScanIndex.R
R/getSnpIndex.R
R/getVariantInclude.R
R/king2mat.R
R/pcair.R
R/pcairPartition.R
R/pcrelate.R
R/pcrelateMakeGRM.R
R/pcrelateReadInbreed.R
R/pcrelateReadKinship.R
R/plot.pcair.R
R/prepareGenotype.R
R/print.pcair.R
R/print.summary.pcair.R
R/subsetCholSigmaInv.R
R/summary.pcair.R
R/varCompCI.R
build
build/vignette.rds
data
data/HapMap_ASW_MXL_KINGmat.rda
inst
inst/NEWS.Rd
inst/doc
inst/doc/assoc_test.R
inst/doc/assoc_test.Rmd
inst/doc/assoc_test.html
inst/doc/pcair.R
inst/doc/pcair.Rmd
inst/doc/pcair.html
inst/extdata
inst/extdata/HapMap_ASW_MXL_geno.gds
inst/extdata/HapMap_ASW_MXL_pcrelate.gds
inst/extdata/MXL_ASW.kin
inst/extdata/MXL_ASW.kin0
inst/unitTests
inst/unitTests/test_SeqVarData.R
inst/unitTests/test_assocTestSeq.R
inst/unitTests/test_king2mat.R
inst/unitTests/test_pcair.R
inst/unitTests/test_pcairPartition.R
inst/unitTests/test_pcrelate.R
man
man/GENESIS-package.Rd
man/HapMap_ASW_MXL_KINGmat.Rd
man/admixMapMM.Rd
man/assocTestMM.Rd
man/assocTestSeq.Rd
man/assocTestSeqWindow.Rd
man/fitNullMM.Rd
man/fitNullReg.Rd
man/king2mat.Rd
man/pcair.Rd
man/pcairPartition.Rd
man/pcrelate.Rd
man/pcrelateMakeGRM.Rd
man/pcrelateReadInbreed.Rd
man/pcrelateReadKinship.Rd
man/plot.pcair.Rd
man/varCompCI.Rd
tests
tests/runTests.R
vignettes
vignettes/assoc_test.Rmd
vignettes/pcair.Rmd
GENESIS documentation built on May 20, 2017, 9:32 p.m.