Files in naglemi/mtmcskat
Multi-Threaded Monte Carlo Sequence Kernel Association Test (MTMC-SKAT)
.DS_Store
.Rbuildignore
.Renviron
.github/workflows/r.yml
.gitignore
.travis.yml
DESCRIPTION
LICENSE.md
NAMESPACE
R/MTMCSKAT_workflow.R
R/MTMCSKAT_workflow_pre_allocate_only.R
R/MTSKAT_workflow.R
R/SKAT_one_window.R
R/bound_window.R
R/calculate_SKAT_empirical_p.R
R/calculate_max_perm_per_core.R
R/chunk_windows.R
R/compare_plots.R
R/convert_to_Z.R
R/data.R
R/extract_window.R
R/map_SKAT_nm.R
R/mappable_SKAT.R
R/mtmcskat_SNPs.R
R/mtskat.R
R/post_process_master_output.R
R/pre_allocate.R
R/re_allocate_windows.R
R/select_windows_range_p.R
R/submit_batch.R
R/subset_list_of_lists.R
R/tally_p_null.R
R/workflow_utils.R
README.Rmd
README.md
Rplots.pdf
SKATMCMT.Rproj
bigdata/poplar_SNPs_Chr10_14460to14550kb.traw
data/.DS_Store
data/sample_SNP_window.rda
data/sample_SNP_window_processed.rda
data/sample_mtmcskat_results.rda
data/sample_mtmcskatnm1_results.rda
data/sample_mtmcskatnm2_results.rda
data/sample_p_null_tallies.rda
data/sample_re_allocated_SNP_windows.rda
data/sample_window_list.rda
data/small_covariates.rda
data/small_mtskat_results.rda
data/small_phenodata.rda
data/small_pre_allocated_windows.rda
data/small_pre_allocated_windows_processed.rda
inst/extdata/TDZ_shoot_area.plink.pheno
inst/extdata/TDZ_shoot_area_200genotypes.pheno
inst/extdata/poplar_200genotypes_14490to14520kb.traw
inst/extdata/poplar_PCs_covariates.tbt
inst/extdata/poplar_PCs_covariates_200genotypes.tbt
inst/extdata/shoot_5w.header.pheno
man/MTMCSKAT_workflow.Rd
man/MTMCSKAT_workflow_pre_allocate_only.Rd
man/SKAT_one_window.Rd
man/benchmark_nm.Rd
man/calculate_SKAT_empirical_p.Rd
man/calculate_max_perm_per_core.Rd
man/chunk_windows.Rd
man/determine_n_permutations.Rd
man/determine_subset_pval_boundaries.Rd
man/extract_window.Rd
man/mappable_SKAT.Rd
man/mtmcskat_NullModels.Rd
man/mtskat.Rd
man/p_empirical_from_tally.Rd
man/pre_allocate.Rd
man/re_allocate_windows.Rd
man/sample_SNP_window.Rd
man/sample_SNP_window_processed.Rd
man/sample_mtmcskat_results.Rd
man/sample_mtmcskatnm1_results.Rd
man/sample_mtmcskatnm2_results.Rd
man/sample_p_null_tallies.Rd
man/sample_re_allocated_SNP_windows.Rd
man/sample_window_list.Rd
man/select_windows_range_p.Rd
man/small_covariates.Rd
man/small_mtskat_results.Rd
man/small_phenodata.Rd
man/small_pre_allocated_windows.Rd
man/small_pre_allocated_windows_processed.Rd
man/subset_list_of_lists.Rd
man/tally_p_null.Rd
pre_allocated_dir/poplar_SNPs_Chr10_14460to14550kb.3000bp_win.rds
tests/testthat.R
tests/testthat/dummy/poplar_200genotypes_14490to14520kb.3000bp_win.rds
tests/testthat/dummy542/poplar_200genotypes_14490to14520kb.3000bp_win.rds
tests/testthat/dummy89e2/poplar_200genotypes_14490to14520kb.3000bp_win.rds
tests/testthat/test-empirical_p.R
tests/testthat/test-extract_window.R
tests/testthat/test-mtmcskat.R
tests/testthat/test-mtskat.R
tests/testthat/test-re_allocate_windows.R
vignettes/.gitignore
vignettes/GWAS_with_mtmcskat.Rmd
vignettes/GWAS_with_mtmcskat.md
wrappers/SLURMcall_c1_Transf_Deploy_Resid_Approach.ipynb
wrappers/batch.R
wrappers/batch_mt_only.R
wrappers/call.sh
wrappers/call_loop.R
wrappers/deploy.R
wrappers/mtmcskat_wrapper.R
wrappers/test_plots.R
wrappers/test_wrapper.sh
wrappers/which_jobs_finished.R
