Introduction | The theory behind BREADR | Processing your data | Processing only pairs within groups to save computational effort | Calling degrees of relatedness from counts | Assessing if groups can be merged | Visualising overall relatedness patterns | Visualising the relatedness information for two individuals | Binomial tests for degrees of relatedness | Sensitivity of the results to the prior distribution | Acknowledgements
Package: BREADR 1.0.4
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_1.0.4.tar.gz
BREADR_1.0.4.zip(r-4.7-any)BREADR_1.0.4.zip(r-4.6-any)BREADR_1.0.4.zip(r-4.5-any)
BREADR_1.0.4.tgz(r-4.6-any)BREADR_1.0.4.tgz(r-4.5-any)
BREADR_1.0.4.tar.gz(r-4.7-any)BREADR_1.0.4.tar.gz(r-4.6-any)
BREADR_1.0.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BREADR/json (API)
| # Install 'BREADR' in R: |
| install.packages('BREADR', repos = c('https://jonotuke.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jonotuke/breadr/issues
Pkgdown/docs site:https://jonotuke.github.io
Datasets:
- counts_example - Counts_example
- relatedness_example - Relatedness_example
Last updated from:ed27851c7a. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 200 | ||
| source / vignettes | OK | 430 | ||
| linux-release-x86_64 | OK | 193 | ||
| macos-release-arm64 | OK | 100 | ||
| macos-oldrel-arm64 | OK | 95 | ||
| windows-devel | OK | 120 | ||
| windows-release | OK | 165 | ||
| windows-oldrel | OK | 106 | ||
| wasm-release | OK | 164 |
Exports:%>%callRelatednessget_column_newplotDOUGHplotLOAFplotSLICEpriorSensitivityprocessEigenstratprocessEigenstrat_oldread_indread_snpsaveSLICESsim_genosplit_linetest_degree
Dependencies:abindafexbackportsBayesFactorbayestestRbitbit64bootbroomBWStestcachemcarcarDataclicliprcodacolorspacecontfraccorrelationcorrplotcowplotcpp11crayondata.tabledatawizardDerivdescdeSolvedoBydplyreffectsizeellipticfarverfastmapforcatsforecastFormulafracdiffgenericsggcorrplotggplot2ggpubrggrepelggsciggsideggsignifggstatsplotgluegmpgridExtragtablehmshypergeoinsightisobandkSampleslabelinglatticelifecyclelme4lmerTestlmtestmagrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvminqamodelrmultcompViewmvtnormnlmenloptrnnetnumDerivpaletteerparameterspatchworkpbapplypbkrtestperformancepillarpkgconfigplyrPMCMRpluspolynomprettyunitsprismaticprogresspurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRdpackreadrreformulasrematch2reshapereshape2rlangRmpfrrstantoolsrstatixrstudioapiS7scalesSparseMstatsExpressionsstringistringrSuppDistssurvivaltibbletidyrtidyselecttimeDatetzdburcautf8vctrsviridisLitevroomwithrWRS2zoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| callRelatedness | callRelatedness |
| counts_example | counts_example |
| get column | get_column_new |
| plotDOUGH | plotDOUGH |
| plotLOAF | plotLOAF |
| plotSLICE | plotSLICE |
| priorSensitivity | priorSensitivity |
| 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 |
