Files in mrc-ide/MIPanalyzer
Filtering and analysis of MIP data
.DS_Store
.Rbuildignore
.github/.gitignore
.github/workflows/checks_develop.yaml
.github/workflows/checks_master.yaml
.gitignore
DESCRIPTION
LICENSE
MIPanalyzer.Rproj
NAMESPACE
R/.Rapp.history
R/MIPanalyzer.R
R/RcppExports.R
R/analysis_clustering.R
R/analysis_distance.R
R/assertions_v5.R
R/data_filtering.R
R/data_wrangling.R
R/main.R
R/mipanalyzer_biallelic.R
R/mipanalyzer_multiallelic.R
R/misc_v2.R
R/package.R
R/probability_v1.R
R/simulation.R
README.Rmd
README.md
R_ignore/.DS_Store
_pkgdown.yml
docs/.DS_Store
docs/404.html
docs/LICENSE-text.html
docs/articles/.DS_Store
docs/articles/PCA_variance.png
docs/articles/PCOA_scatter.png
docs/articles/filtering_data.html
docs/articles/filtering_data_files/figure-html/unnamed-chunk-11-1.png
docs/articles/filtering_data_files/figure-html/unnamed-chunk-13-1.png
docs/articles/genetic_distances.html
docs/articles/genetic_distances_files/figure-html/unnamed-chunk-5-1.png
docs/articles/genetic_distances_files/figure-html/unnamed-chunk-6-1.png
docs/articles/genetic_distances_files/figure-html/unnamed-chunk-7-1.png
docs/articles/genetic_distances_files/figure-html/unnamed-chunk-8-1.png
docs/articles/genetic_distances_files/figure-html/unnamed-chunk-9-1.png
docs/articles/index.html
docs/articles/installation.html
docs/articles/introduction.html
docs/articles/introduction_files/.DS_Store
docs/articles/introduction_files/figure-html/coverage plot-1.png
docs/articles/introduction_files/figure-html/pca contribution-1.png
docs/articles/introduction_files/figure-html/plot loci filtering-1.png
docs/articles/introduction_files/figure-html/plot sample coverage-1.png
docs/articles/introduction_files/figure-html/wsaf-1.png
docs/articles/structure_analysis.html
docs/articles/structure_analysis_files/figure-html/unnamed-chunk-6-1.png
docs/articles/structure_analysis_files/figure-html/unnamed-chunk-9-1.png
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/.DS_Store
docs/reference/MIPanalyzer.html
docs/reference/MIPanalyzerbi2vcfR.html
docs/reference/Pf_chrom_lengths.html
docs/reference/Rplot001.png
docs/reference/assignGTfrombiWSNRAF.html
docs/reference/assignGTfrombiWSRAF.html
docs/reference/check_MIPanalyzer_loaded.html
docs/reference/explore_filter_coverage_loci.html
docs/reference/explore_filter_coverage_samples.html
docs/reference/filter_counts.html
docs/reference/filter_coverage_loci.html
docs/reference/filter_coverage_samples.html
docs/reference/filter_loci.html
docs/reference/filter_loci_invariant.html
docs/reference/filter_overcounts.html
docs/reference/filter_samples.html
docs/reference/filter_wsaf.html
docs/reference/get_IBS_distance.html
docs/reference/get_IB_mixture.html
docs/reference/get_genomic_distance.html
docs/reference/get_spatial_distance.html
docs/reference/get_wsaf.html
docs/reference/inbreeding_mle.html
docs/reference/index.html
docs/reference/is.mipanalyzer_biallelic.html
docs/reference/is.mipanalyzer_multiallelic.html
docs/reference/lonlat_to_bearing.html
docs/reference/mipanalyzer_biallelic_to_vcfR.html
docs/reference/mipanalyzer_file.html
docs/reference/pca_wsaf.html
docs/reference/pcoa_genomic_distance.html
docs/reference/pipe.html
docs/reference/plot_coverage.html
docs/reference/plot_distance.html
docs/reference/plot_map.html
docs/reference/plot_pca.html
docs/reference/plot_pca_contribution.html
docs/reference/plot_pca_variance.html
docs/reference/plot_pcoa.html
docs/reference/plot_wsaf.html
docs/reference/print.mipanalyzer_biallelic.html
docs/reference/print.mipanalyzer_multiallelic.html
docs/reference/print_full.html
docs/reference/rbetabinom.html
docs/reference/rdirichlet.html
docs/reference/sim_biallelic.html
docs/reference/summary.mipanalyzer_biallelic.html
docs/reference/summary.mipanalyzer_multiallelic.html
docs/reference/vcf2mipanalyzer_biallelic.html
docs/reference/vcf2mipanalyzer_multiallelic.html
docs/reference/vcf_to_mipanalyzer_biallelic.html
docs/reference/vcf_to_mipanalyzer_multiallelic.html
docs/sitemap.xml
index.md
inst/.DS_Store
inst/extdata/.DS_Store
inst/extdata/DRC_pf3k_filtered.vcf
inst/extdata/dat_biallelic.rds
man/MIPanalyzer.Rd
man/Pf_chrom_lengths.Rd
man/check_MIPanalyzer_loaded.Rd
man/explore_filter_coverage_loci.Rd
man/explore_filter_coverage_samples.Rd
man/filter_counts.Rd
man/filter_coverage_loci.Rd
man/filter_coverage_samples.Rd
man/filter_loci.Rd
man/filter_loci_invariant.Rd
man/filter_overcounts.Rd
man/filter_samples.Rd
man/filter_wsaf.Rd
man/get_IBS_distance.Rd
man/get_IB_mixture.Rd
man/get_genomic_distance.Rd
man/get_spatial_distance.Rd
man/get_wsaf.Rd
man/inbreeding_mle.Rd
man/is.mipanalyzer_biallelic.Rd
man/is.mipanalyzer_multiallelic.Rd
man/lonlat_to_bearing.Rd
man/mipanalyzer_biallelic_to_vcfR.Rd
man/mipanalyzer_file.Rd
man/pca_wsaf.Rd
man/pcoa_genomic_distance.Rd
man/plot_coverage.Rd
man/plot_distance.Rd
man/plot_map.Rd
man/plot_pca.Rd
man/plot_pca_contribution.Rd
man/plot_pca_variance.Rd
man/plot_pcoa.Rd
man/plot_wsaf.Rd
man/print.mipanalyzer_biallelic.Rd
man/print.mipanalyzer_multiallelic.Rd
man/rbetabinom.Rd
man/rdirichlet.Rd
man/sim_biallelic.Rd
man/summary.mipanalyzer_biallelic.Rd
man/summary.mipanalyzer_multiallelic.Rd
man/vcf_to_mipanalyzer_biallelic.Rd
man/vcf_to_mipanalyzer_multiallelic.Rd
src/.DS_Store
src/.gitignore
src/RcppExports.cpp
src/main.cpp
src/main.h
src/misc_v2.cpp
src/misc_v2.h
tests/testthat.R
tests/testthat/test-assertions_v4.R
tests/testthat/test-main.R
vignettes/.gitignore
vignettes/PCA_scatter.png
vignettes/PCA_variance.png
vignettes/PCOA_scatter.png
vignettes/filtering_data.Rmd
vignettes/genetic_distances.Rmd
vignettes/installation.Rmd
vignettes/structure_analysis.Rmd
