Package: BREADR 1.0.2
Jono Tuke
BREADR: Estimates Degrees of Relatedness (Up to the Second Degree) for Extreme Low-Coverage Data
The goal of the package is to provide an easy-to-use method for estimating degrees of relatedness (up to the second degree) for extreme low-coverage data. The package also allows users to quantify and visualise the level of confidence in the estimated degrees of relatedness.
Authors:
BREADR_1.0.2.tar.gz
BREADR_1.0.2.tar.gz(r-4.5-noble)BREADR_1.0.2.tar.gz(r-4.4-noble)
BREADR_1.0.2.tgz(r-4.4-emscripten)BREADR_1.0.2.tgz(r-4.3-emscripten)
BREADR.pdf |BREADR.html✨
BREADR/json (API)
NEWS
| # Install 'BREADR' in R: |
| install.packages('BREADR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jonotuke/breadr/issues
Pkgdown site:https://jonotuke.github.io
- counts_example - Counts_example
- relatedness_example - Relatedness_example
Last updated 4 months agofrom:8e832a074b. Checks:2 OK. Indexed: no.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 08 2025 |
| R-4.5-linux | OK | Jan 08 2025 |
Exports:%>%callRelatednessget_column_newplotLOAFplotSLICEprocessEigenstratprocessEigenstrat_oldread_indread_snpsaveSLICESsim_genosplit_linetest_degree
Dependencies:abindbackportsbitbit64bootbroomcarcarDataclicliprcolorspacecorrplotcowplotcpp11crayondata.tableDerivdoBydplyrfansifarverforcatsFormulagenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehmsisobandlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmatrixStatsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpolynomprettyunitsprogresspurrrquantregR6RColorBrewerRcppRcppEigenreadrrlangrstatixscalesSparseMstringistringrsurvivaltibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| callRelatedness | callRelatedness |
| counts_example | counts_example |
| get column | get_column_new |
| plotLOAF | plotLOAF |
| plotSLICE | plotSLICE |
| process Eigenstrat data - alternative version | processEigenstrat |
| process Eigenstrat data | processEigenstrat_old |
| read_ind | read_ind |
| read_snp | read_snp |
| relatedness_example | relatedness_example |
| saveSLICES | saveSLICES |
| sim_geno | sim_geno |
| split line | split_line |
| test_degree | test_degree |
