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.

AuthorMatthew P. Conomos and Timothy Thornton
Date of publicationNone
MaintainerMatthew P. Conomos <mconomos@uw.edu>
LicenseGPL-3
Version2.4.0

View on Bioconductor

Functions

assocTestMM Man page
assocTestSeq Man page
assocTestSeqWindow Man page
fitNullMM Man page
fitNullReg Man page
GENESIS Man page
GENESIS-package Man page
HapMap_ASW_MXL_KINGmat Man page
king2mat Man page
pcair Man page
pcairPartition Man page
pcrelate Man page
pcrelateMakeGRM Man page
pcrelateReadInbreed Man page
pcrelateReadKinship Man page
plot.pcair Man page
print.pcair Man page
print.summary.pcair Man page
summary.pcair Man page
varCompCI Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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