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

.Rbuildignore
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
NAMESPACE
R/admixMap.R R/assocTestAggregate.R R/assocTestSingle.R R/bigQF.R R/calcAIcovMatsFunctions.R R/calcLQ.R R/calcSQ.R R/computeVSIF.R R/createDesignMatrix.R R/effectAllele.R R/fitNullModel.R R/fitNullModel_internal.R R/iterateAIREMLworkingY.R R/jointScoreTest.R R/kin2gds.R R/makeSparseMatrix.R R/nullModelAsMatrix.R R/nullModelFastScore.R R/nullModelInvNorm.R R/nullModelSubset.R R/nullModelTestPrep.R R/pcair.R R/pcairPartition.R R/pcair_S3methods.R R/pcrelate.R R/prepareOutputForNullModel.R R/runAIREMLgaussian.R R/runAIREMLother.R R/runWLS.R R/spa.R R/testGeno.R R/testSingleVarianceComponent.R R/updateNullModCond.R R/util_methods.R R/utils.R R/varCompCI.R R/variantSetTests.R README.md
data/HapMap_ASW_MXL_KINGmat.rda
data/sample_annotation_1KG.rda
inst/CITATION
inst/NEWS.Rd
inst/extdata/1KG/1KG_phase3_subset_chr1.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr10.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr11.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr12.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr13.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr14.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr15.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr16.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr17.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr18.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr19.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr2.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr20.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr21.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr22.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr3.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr4.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr5.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr6.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr7.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr8.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chr9.vcf.gz
inst/extdata/1KG/1KG_phase3_subset_chrX.vcf.gz
inst/extdata/HapMap.seg
inst/extdata/HapMap_ASW_MXL_geno.gds
inst/extdata/HapMap_ASW_MXL_local_afr.gds
inst/extdata/HapMap_ASW_MXL_local_amer.gds
inst/extdata/HapMap_ASW_MXL_local_eur.gds
inst/extdata/HapMap_ASW_MXL_pcrelate.gds
inst/extdata/MXL_ASW.kin
inst/extdata/MXL_ASW.kin0
man/GENESIS-package.Rd man/HapMap_ASW_MXL_KINGmat.Rd man/admixMap.Rd man/assocTestAggregate.Rd man/assocTestSingle.Rd man/computeVSIF.Rd man/defunct.Rd man/effectAllele.Rd man/fitNullModel.Rd man/jointScoreTest.Rd man/kin2gds.Rd man/kingToMatrix.Rd man/makeSparseMatrix.Rd man/pcair.Rd man/pcairPartition.Rd man/pcrelate.Rd man/pcrelateToMatrix.Rd man/plot.pcair.Rd man/print.pcair.Rd man/sample_annotation_1KG.Rd man/varCompCI.Rd
src/fht.c
tests/testthat.R tests/testthat/helper_nullInputs.R tests/testthat/helper_testData.R tests/testthat/helper_testGenoData.R tests/testthat/old_test_GENESIS.R tests/testthat/old_test_SeqVarData.R tests/testthat/old_test_assocTestMM.R tests/testthat/old_test_pcrelate.R tests/testthat/old_test_pcrelate2.R tests/testthat/test_VSIF.R tests/testthat/test_admixMap.R tests/testthat/test_assocTestAggregate.R tests/testthat/test_assocTestAggregate_GenotypeIterator.R tests/testthat/test_assocTestSingle.R tests/testthat/test_assocTestSingle_GenotypeIterator.R tests/testthat/test_assoc_parallel.R tests/testthat/test_covMatList.R tests/testthat/test_effectAllele.R tests/testthat/test_fastScoreSE.R tests/testthat/test_imputed.R tests/testthat/test_jointScoreTest.R tests/testthat/test_kingToMatrix.R tests/testthat/test_makeSparseMatrix.R tests/testthat/test_nullModel.R tests/testthat/test_null_model_Matrix.R tests/testthat/test_null_model_WLS_regression.R tests/testthat/test_null_model_glmm.R tests/testthat/test_null_model_linear_regression.R tests/testthat/test_null_model_lmm.R tests/testthat/test_null_model_logistic_regression.R tests/testthat/test_null_prep.R tests/testthat/test_pcair.R tests/testthat/test_pcairPartition.R tests/testthat/test_pcrelate.R tests/testthat/test_pcrelate_parallel.R tests/testthat/test_single_var_association_tests.R tests/testthat/test_utils.R tests/testthat/test_variant_set.R tests/testthat/testdata/generate_data_old_nullmod.R
tests/testthat/testdata/old_nullmod_glm.rds
tests/testthat/testdata/old_nullmod_glmm.rds
tests/testthat/testdata/old_nullmod_lm.rds
tests/testthat/testdata/old_nullmod_lmm.rds
tests/testthat/testdata/old_nullmod_wls.rds
tests/testthat/tmp_test_update_outcome.R vignettes/assoc_test.Rmd vignettes/assoc_test_seq.Rmd vignettes/pcair.Rmd
UW-GAC/GENESIS documentation built on June 14, 2022, 3:05 p.m.