Files in GenuityScience/topr
Create Custom Plots for Viewing Genetic Association Results
.Rbuildignore
.gitignore
CRAN-SUBMISSION
DESCRIPTION
LICENSE.md
Makefile
NAMESPACE
NEWS.md
R/dat_checks.R
R/data.R
R/deprec_funcs.R
R/effectplot.R
R/exonplot.R
R/geneplot.R
R/get_genes_and_annotation.R
R/get_plots.R
R/globals.R
R/locuszoomplot.R
R/manhattan.R
R/miscellaneous.R
R/plot_functions.R
R/qqtopr.R
R/regionplot.R
R/setters_and_getters.R
R/sysdata.rda
R/topr.R
R/utils-pipe.R
README.html
README.md
cran-comments.md
data/CD_FINNGEN.rda
data/CD_UKBB.rda
data/R2_CD_UKBB.rda
data/UC_UKBB.rda
doc/manhattan.R
doc/manhattan.html
doc/manhattan.rmd
doc/regionplot.R
doc/regionplot.html
doc/regionplot.rmd
doc/topr.R
doc/topr.Rmd
doc/topr.html
docs/404.html
docs/LICENSE.html
docs/articles/figures/locuszoom.jpg
docs/articles/figures/locuszoom_annotate.jpg
docs/articles/figures/manhattan.jpg
docs/articles/figures/manhattan_annotate.jpg
docs/articles/figures/manhattan_chr1.jpg
docs/articles/figures/manhattan_genes.jpg
docs/articles/figures/manhattan_multi.jpg
docs/articles/figures/manhattan_multi_ntop.jpg
docs/articles/figures/regionplot.jpg
docs/articles/figures/regionplot_annotate.jpg
docs/articles/figures/regionplot_annotate_vline.jpg
docs/articles/figures/regionplot_multi.jpg
docs/articles/index.html
docs/articles/input_dataset.html
docs/articles/input_datasets.html
docs/articles/manhattan.html
docs/articles/manhattan_files/figure-html/unnamed-chunk-10-1.png
docs/articles/regionplot.html
docs/articles/topr.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/CD_FINNGEN.html
docs/reference/CD_UKBB.html
docs/reference/ENSEXONS.html
docs/reference/ENSGENES.html
docs/reference/R2_CD_UKBB.html
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/UC_UKBB.html
docs/reference/annotate_with_nearest_gene.html
docs/reference/create_snpset.html
docs/reference/create_snpset_code.html
docs/reference/dat_column_check_and_set.html
docs/reference/effect_plot.html
docs/reference/effectplot-1.png
docs/reference/effectplot.html
docs/reference/figures/README-unnamed-chunk-10-1.png
docs/reference/figures/README-unnamed-chunk-11-1.png
docs/reference/figures/README-unnamed-chunk-12-1.png
docs/reference/figures/README-unnamed-chunk-13-1.png
docs/reference/figures/README-unnamed-chunk-14-1.png
docs/reference/figures/README-unnamed-chunk-15-1.png
docs/reference/figures/README-unnamed-chunk-16-1.png
docs/reference/figures/README-unnamed-chunk-17-1.png
docs/reference/figures/README-unnamed-chunk-18-1.png
docs/reference/figures/README-unnamed-chunk-19-1.png
docs/reference/figures/README-unnamed-chunk-20-1.png
docs/reference/figures/README-unnamed-chunk-21-1.png
docs/reference/figures/README-unnamed-chunk-22-1.png
docs/reference/figures/README-unnamed-chunk-23-1.png
docs/reference/figures/README-unnamed-chunk-24-1.png
docs/reference/figures/README-unnamed-chunk-25-1.png
docs/reference/figures/README-unnamed-chunk-26-1.png
docs/reference/figures/README-unnamed-chunk-5-1.png
docs/reference/figures/README-unnamed-chunk-6-1.png
docs/reference/figures/README-unnamed-chunk-7-1.png
docs/reference/figures/README-unnamed-chunk-8-1.png
docs/reference/figures/README-unnamed-chunk-9-1.png
docs/reference/figures/topr.gif
docs/reference/figures/topr_v.1.1.0.gif
docs/reference/flip_to_positive_allele_for_dat1.html
docs/reference/get_best_snp_per_MB.html
docs/reference/get_gene.html
docs/reference/get_gene_coords.html
docs/reference/get_genes_by_Gene_Symbol.html
docs/reference/get_genes_in_region.html
docs/reference/get_lead_snps.html
docs/reference/get_overlapping_snps_by_pos.html
docs/reference/get_snps_within_region.html
docs/reference/get_snpset.html
docs/reference/get_snpset_code.html
docs/reference/get_top_hit.html
docs/reference/get_top_snp.html
docs/reference/get_topr_colors.html
docs/reference/index.html
docs/reference/locuszoom.html
docs/reference/manhattan-1.png
docs/reference/manhattan.html
docs/reference/match_alleles.html
docs/reference/match_by_alleles.html
docs/reference/match_by_pos.html
docs/reference/pipe.html
docs/reference/qqplot.html
docs/reference/qqtopr.html
docs/reference/regionplot.html
docs/reference/topr-1.png
docs/reference/topr-2.png
docs/reference/topr.html
docs/sitemap.xml
man/CD_FINNGEN.Rd
man/CD_UKBB.Rd
man/R2_CD_UKBB.Rd
man/UC_UKBB.Rd
man/annotate_with_nearest_gene.Rd
man/create_snpset.Rd
man/create_snpset_code.Rd
man/effect_plot.Rd
man/effectplot.Rd
man/figures/README-unnamed-chunk-10-1.png
man/figures/README-unnamed-chunk-11-1.png
man/figures/README-unnamed-chunk-12-1.png
man/figures/README-unnamed-chunk-13-1.png
man/figures/README-unnamed-chunk-14-1.png
man/figures/README-unnamed-chunk-15-1.png
man/figures/README-unnamed-chunk-16-1.png
man/figures/README-unnamed-chunk-17-1.png
man/figures/README-unnamed-chunk-18-1.png
man/figures/README-unnamed-chunk-19-1.png
man/figures/README-unnamed-chunk-20-1.png
man/figures/README-unnamed-chunk-21-1.png
man/figures/README-unnamed-chunk-22-1.png
man/figures/README-unnamed-chunk-23-1.png
man/figures/README-unnamed-chunk-24-1.png
man/figures/README-unnamed-chunk-25-1.png
man/figures/README-unnamed-chunk-26-1.png
man/figures/README-unnamed-chunk-5-1.png
man/figures/README-unnamed-chunk-6-1.png
man/figures/README-unnamed-chunk-7-1.png
man/figures/README-unnamed-chunk-8-1.png
man/figures/README-unnamed-chunk-9-1.png
man/figures/locuszoom.png
man/figures/logo.svg
man/figures/manhattanExtra.png
man/figures/manhattan_colored_peaks.png
man/figures/manhattan_colored_peaks2.png
man/figures/manhattan_wide_1080_high.gif
man/figures/topr_v.1.1.0.gif
man/flip_to_positive_allele_for_dat1.Rd
man/get_best_snp_per_MB.Rd
man/get_gene.Rd
man/get_gene_coords.Rd
man/get_genes_by_Gene_Symbol.Rd
man/get_genes_in_region.Rd
man/get_lead_snps.Rd
man/get_overlapping_snps_by_pos.Rd
man/get_sign_and_sugg_loci.Rd
man/get_snps_within_region.Rd
man/get_snpset.Rd
man/get_snpset_code.Rd
man/get_top_snp.Rd
man/get_topr_colors.Rd
man/locuszoom.Rd
man/manhattan.Rd
man/manhattanExtra.Rd
man/match_alleles.Rd
man/match_by_alleles.Rd
man/match_by_pos.Rd
man/pipe.Rd
man/qqtopr.Rd
man/regionplot.Rd
man/topr.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
tests/testthat.R
tests/testthat/test-locuszoom.R
tests/testthat/test-manhattan.R
tests/testthat/test-regionplot.R
tests/testthat/test-test-datasets.R
tests/testthat/test-utils.R
topr.Rproj
vignettes/.gitignore
vignettes/articles/locuszoom.Rmd
vignettes/articles/manhattanExtra.Rmd
vignettes/articles/moreManhattan.Rmd
vignettes/figures/locuszoom.jpg
vignettes/figures/locuszoom_annotate.jpg
vignettes/figures/manhattan.jpg
vignettes/figures/manhattan_annotate.jpg
vignettes/figures/manhattan_chr1.jpg
vignettes/figures/manhattan_genes.jpg
vignettes/figures/manhattan_multi.jpg
vignettes/figures/manhattan_multi_ntop.jpg
vignettes/figures/manhattan_multi_ntop_tidy.jpg
vignettes/figures/manhattan_multi_ntop_tidy_grey.jpg
vignettes/figures/manhattan_multi_ntop_tidy_vline.jpg
vignettes/figures/regionplot.jpg
vignettes/figures/regionplot_annotate.jpg
vignettes/figures/regionplot_annotate_vline.jpg
vignettes/figures/regionplot_multi.jpg
vignettes/input_datasets.nb.html
vignettes/manhattan.nb.html
vignettes/manhattan.rmd
vignettes/regionplot.nb.html
vignettes/regionplot.rmd
vignettes/topr.Rmd
vignettes/topr.nb.html
