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

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
Date of publication
None
Maintainer
Matthew P. Conomos <mconomos@uw.edu>
License
GPL-3
Version
2.4.0

View on Bioconductor

Man pages

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

Files in this package

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