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

DESCRIPTION
README.md
NAMESPACE
inst/NEWS.Rd
inst/doc/pcair.Rmd
inst/doc/assoc_test.html
inst/doc/pcair.R
inst/doc/assoc_test_seq.html
inst/doc/pcair.html
inst/doc/assoc_test.Rmd inst/doc/assoc_test_seq.R inst/doc/assoc_test.R inst/doc/assoc_test_seq.Rmd
inst/extdata/HapMap.seg
inst/extdata/MXL_ASW.kin0
inst/extdata/HapMap_ASW_MXL_geno.gds
inst/extdata/MXL_ASW.kin
inst/extdata/HapMap_ASW_MXL_pcrelate.gds
inst/extdata/1KG/1KG_phase3_subset_chr10.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr17.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr16.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr8.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr13.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr9.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr14.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chrX.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr19.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr6.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr3.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr7.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr22.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr5.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr2.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr1.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr12.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr21.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr4.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr11.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr20.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr15.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr18.vcf.gz
vignettes/pcair.Rmd vignettes/assoc_test.Rmd vignettes/assoc_test_seq.Rmd R/runAIREMLgaussian.R R/pcairPartition.R R/assocTestSingle.R R/nullModelTestPrep.R R/fitNullModel_internal.R R/runWLS.R R/calcAIcovMatsFunctions.R R/admixMapMM.R R/pcrelate2.R R/pcrelateReadInbreed.R R/pcrelateReadKinship.R R/pcair.R R/varCompCI.R R/utils.R R/kin2gds.R R/fitNullReg.R R/createDesignMatrix.R R/SeqVarData_utils.R R/pcair_S3methods.R R/prepareGenotype.R R/assocTestSeq.R R/calcLQ.R R/admixMap.R R/alleleFreq.R R/nullModelAsMatrix.R R/runAIREMLother.R R/updateNullModOutcome.R R/getBlocks.R R/pcrelateMakeGRM.R R/variantSetTests.R R/fitNullMM.R R/assocTestAggregate.R R/util_methods.R R/testGeno.R R/fitNullModel.R R/makeSparseMatrix.R R/nullModelSubset.R R/updateNullModCond.R R/getScanIndex.R R/assocTestMM.R R/calcSQ.R R/getSnpIndex.R R/pcrelate.R R/iterateAIREMLworkingY.R R/prepareOutputForNullModel.R R/testSingleVarianceComponent.R R/king2mat.R man/makeSparseMatrix.Rd man/king2mat.Rd man/assocTestMM.Rd man/print.pcair.Rd man/fitNullMM.Rd man/assocTestAggregate.Rd man/pcrelateReadInbreed.Rd man/admixMapMM.Rd man/HapMap_ASW_MXL_KINGmat.Rd man/pcrelate.Rd man/pcairPartition.Rd man/pcrelateToMatrix.Rd man/fitNullModel.Rd man/deprecated.Rd man/pcrelateMakeGRM.Rd man/sample_annotation_1KG.Rd man/fitNullReg.Rd man/plot.pcair.Rd man/kingToMatrix.Rd man/varCompCI.Rd man/assocTestSingle.Rd man/kin2gds.Rd man/GENESIS-package.Rd man/pcrelateReadKinship.Rd man/admixMap.Rd man/pcrelate_deprecated.Rd man/pcair.Rd man/defunct.Rd
build/vignette.rds
tests/testthat.R tests/testthat/test_null_model_glmm.R tests/testthat/test_makeSparseMatrix.R tests/testthat/helper_testGenoData.R tests/testthat/test_covMatList.R tests/testthat/old_test_assocTestMM.R tests/testthat/test_assocTestSingle_GenotypeIterator.R tests/testthat/test_null_model_Matrix.R tests/testthat/test_pcairPartition.R tests/testthat/test_pcair.R tests/testthat/test_kingToMatrix.R tests/testthat/test_pcrelate2.R tests/testthat/old_test_GENESIS.R tests/testthat/helper_testData.R tests/testthat/test_null_model_WLS_regression.R tests/testthat/test_null_model_logistic_regression.R tests/testthat/tmp_test_update_outcome.R tests/testthat/test_variant_set.R tests/testthat/test_single_var_association_tests.R tests/testthat/test_assocTestSingle.R tests/testthat/test_null_model_linear_regression.R tests/testthat/old_test_SeqVarData.R tests/testthat/test_assocTestAggregate.R tests/testthat/test_nullModel.R tests/testthat/test_assocTestAggregate_GenotypeIterator.R tests/testthat/test_null_model_lmm.R tests/testthat/test_null_prep.R tests/testthat/old_test_pcrelate.R tests/testthat/helper_nullInputs.R
data/HapMap_ASW_MXL_KINGmat.rda
data/sample_annotation_1KG.rda
GENESIS documentation built on Nov. 1, 2018, 6:01 p.m.