Files in ollyburren/cupcake
PCA for GWAS
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/.gitignore
R/align_alleles.R
R/burren_imd_13_traits.R
R/cupfunc.R
R/globals.R
R/lyons_egpa.R
R/posterior_lor.R
R/simulate.R
R/variance.R
README.md
_pkgdown.yml
cupcake.Rproj
data/burren_imd_13_traits.RData
data/lyons_egpa.RData
docs/404.html
docs/LICENSE-text.html
docs/articles/create-basis.html
docs/articles/create-basis_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/create-basis_files/figure-html/unnamed-chunk-10-1.png
docs/articles/create-basis_files/figure-html/unnamed-chunk-11-1.png
docs/articles/create-basis_files/figure-html/unnamed-chunk-14-1.png
docs/articles/create-basis_files/header-attrs-2.3/header-attrs.js
docs/articles/index.html
docs/articles/project-basis.html
docs/articles/project-basis_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/project-basis_files/figure-html/unnamed-chunk-7-1.png
docs/articles/project-basis_files/header-attrs-2.3/header-attrs.js
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/LD.html
docs/reference/SNP.manifest.html
docs/reference/add_ref_annotations.html
docs/reference/align_alleles.html
docs/reference/ambiguous.html
docs/reference/basis.trait.proj.html
docs/reference/beta.centers.html
docs/reference/comp.html
docs/reference/compute_seb_proj_var.html
docs/reference/compute_seb_proj_var_sparse.html
docs/reference/compute_shrinkage_metrics.html
docs/reference/control_prior_shape.html
docs/reference/cov_beta.html
docs/reference/create_basis.html
docs/reference/create_ds_matrix.html
docs/reference/e_lor.html
docs/reference/est_a1b1.html
docs/reference/flip_allele.html
docs/reference/fopt.html
docs/reference/get_gwas_data.html
docs/reference/get_seb.html
docs/reference/index.html
docs/reference/logsum.html
docs/reference/lor_constraint.html
docs/reference/lor_f.html
docs/reference/lor_nf.html
docs/reference/lyons_egpa.html
docs/reference/maf_se_estimate.html
docs/reference/maf_se_estimate_sample_size.html
docs/reference/mvs_perm.html
docs/reference/mvs_sigma.html
docs/reference/opt_a1b1.html
docs/reference/p2z.html
docs/reference/post_lor.html
docs/reference/project_basis.html
docs/reference/project_sparse.html
docs/reference/rot.pca.html
docs/reference/se_null.html
docs/reference/shrinkage.html
docs/reference/simulate_beta.html
docs/reference/simulate_study.html
docs/reference/stats.html
docs/reference/use.pca.html
docs/reference/vcf2snpmatrix.html
docs/reference/wakefield_null_pp.html
docs/reference/wakefield_pp.html
docs/reference/ws_shrinkage.html
docs/reference/z2p.html
docs/sitemap.xml
inst/extdata/sparse_imd_basis/gwas_data/.gitignore
inst/extdata/sparse_imd_basis/gwas_data/asthma_demenais.tab
inst/extdata/sparse_imd_basis/gwas_data/cd_delaange.tab
inst/extdata/sparse_imd_basis/gwas_data/cel_dubois.tab
inst/extdata/sparse_imd_basis/gwas_data/ms_imsgc.tab
inst/extdata/sparse_imd_basis/gwas_data/pbc_cordell.tab
inst/extdata/sparse_imd_basis/gwas_data/psc_ji.tab
inst/extdata/sparse_imd_basis/gwas_data/ra_okada.tab
inst/extdata/sparse_imd_basis/gwas_data/sle_bentham.tab
inst/extdata/sparse_imd_basis/gwas_data/t1d_cooper.tab
inst/extdata/sparse_imd_basis/gwas_data/uc_delaange.tab
inst/extdata/sparse_imd_basis/gwas_data/ukbb_neale_srd_sle.tab
inst/extdata/sparse_imd_basis/gwas_data/vitiligo_jin.tab
inst/extdata/sparse_imd_basis/support/.gitignore
inst/extdata/sparse_imd_basis/support/13_trait_sparse_basis.RDS
inst/extdata/sparse_imd_basis/support/13_trait_sparse_basis_noshrink.RDS
inst/extdata/sparse_imd_basis/support/13_trait_sparse_shrinkage.RDS
inst/extdata/sparse_imd_basis/support/13_trait_sparse_trait_manifest.tab
inst/extdata/sparse_imd_basis/support/1KG_reference_genotypes.RDS
inst/extdata/sparse_imd_basis/support/basis-sparse-13-0.999.RData
inst/extdata/sparse_imd_basis/support/basis-sparse-13-imd.RData
inst/extdata/sparse_imd_basis/support/hapmap.ld.tab
inst/extdata/sparse_imd_basis/support/sparse_snp_manifest.RDS
inst/extdata/sparse_imd_basis/support/sparse_trait_manifest.tab
man/LD.Rd
man/SNP.manifest.Rd
man/add_ref_annotations.Rd
man/align_alleles.Rd
man/ambiguous.Rd
man/basis.trait.proj.Rd
man/beta.centers.Rd
man/comp.Rd
man/compute_seb_proj_var.Rd
man/compute_seb_proj_var_sparse.Rd
man/compute_shrinkage_metrics.Rd
man/control_prior_shape.Rd
man/cov_beta.Rd
man/create_basis.Rd
man/create_ds_matrix.Rd
man/e_lor.Rd
man/est_a1b1.Rd
man/flip_allele.Rd
man/fopt.Rd
man/get_gwas_data.Rd
man/get_seb.Rd
man/logsum.Rd
man/lor_constraint.Rd
man/lor_f.Rd
man/lyons_egpa.Rd
man/maf_se_estimate.Rd
man/maf_se_estimate_sample_size.Rd
man/mvs_perm.Rd
man/mvs_sigma.Rd
man/opt_a1b1.Rd
man/p2z.Rd
man/post_lor.Rd
man/project_basis.Rd
man/project_sparse.Rd
man/rot.pca.Rd
man/se_null.Rd
man/shrinkage.Rd
man/simulate_beta.Rd
man/simulate_study.Rd
man/use.pca.Rd
man/vcf2snpmatrix.Rd
man/wakefield_null_pp.Rd
man/wakefield_pp.Rd
man/ws_shrinkage.Rd
man/z2p.Rd
vignettes/create-basis.Rmd
vignettes/project-basis.Rmd
