Files in T-Heide/MLLLP
Maximum Likelihood Assignment of Low-Pass Samples to Trees
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
MLLPT.Rproj
NAMESPACE
R/aaa.R
R/analysis_pipeline.R
R/datasets.R
R/methods.R
R/plotting_methods.R
README.Rmd
README.md
README_files/figure-gfm/edge_position_example-1.png
README_files/figure-gfm/loglik_edge_plus_lp_example-1.png
README_files/figure-gfm/loglik_plus_lp_example-1.png
README_files/figure-gfm/sample_data_lp_example-1.png
README_files/figure-gfm/tree_plus_lp_example-1.png
codecov.yml
data/example_lp_data.RData
docs/404.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/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/add_lowpass_sampled.html
docs/reference/get_mutation_ids_per_edge.html
docs/reference/index.html
docs/reference/plot_lp_loglik.html
docs/reference/plot_lp_loglik_edge.html
docs/reference/plot_sample_data.html
docs/reference/plot_tree-1.png
docs/reference/plot_tree.html
inst/allele_counts.py
inst/extdata/test_mutation.table
man/add_lowpass_sampled.Rd
man/example_lp_data.Rd
man/figures/logo.png
man/get_mutation_ids_per_edge.Rd
man/load_genotyping_file.Rd
man/plot_lp_loglik.Rd
man/plot_lp_loglik_edge.Rd
man/plot_lp_position_edge.Rd
man/plot_sample_data.Rd
man/plot_tree.Rd
man/plot_tree_and_cn_data.Rd
man/reexports.Rd
man/remove_root_tip.Rd
man/set_lp_tiplength.Rd
tests/testthat.R
tests/testthat/data.rda
tests/testthat/expected_example_results.rds
tests/testthat/test-methods.R
