Files in smgogarten/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
