Package: skater 0.1.2
Stephen Turner
skater: Utilities for SNP-Based Kinship Analysis
Utilities for single nucleotide polymorphism (SNP) based kinship analysis testing and evaluation. The 'skater' package contains functions for importing, parsing, and analyzing pedigree data, performing relationship degree inference, benchmarking relationship degree classification, and summarizing identity by descent (IBD) segment data. Package functions and methods are described in Turner et al. (2021) "skater: An R package for SNP-based Kinship Analysis, Testing, and Evaluation" <doi:10.1101/2021.07.21.453083>.
Authors:
skater_0.1.2.tar.gz
skater_0.1.2.zip(r-4.5)skater_0.1.2.zip(r-4.4)skater_0.1.2.zip(r-4.3)
skater_0.1.2.tgz(r-4.4-any)skater_0.1.2.tgz(r-4.3-any)
skater_0.1.2.tar.gz(r-4.5-noble)skater_0.1.2.tar.gz(r-4.4-noble)
skater_0.1.2.tgz(r-4.4-emscripten)skater_0.1.2.tgz(r-4.3-emscripten)
skater.pdf |skater.html✨
skater/json (API)
NEWS
| # Install 'skater' in R: |
| install.packages('skater', repos = c('https://signaturescience.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/signaturescience/skater/issues
Last updated 2 years agofrom:97c2ba52c6. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 26 2024 |
| R-4.5-win | OK | Oct 26 2024 |
| R-4.5-linux | OK | Oct 26 2024 |
| R-4.4-win | OK | Oct 26 2024 |
| R-4.4-mac | OK | Oct 26 2024 |
| R-4.3-win | OK | Oct 26 2024 |
| R-4.3-mac | OK | Oct 26 2024 |
Exports:%>%arrange_idsconfusion_matrixdibblefam2pedibd2kinkin2cmkin2degreeped2kinpairplot_pedigreeread_aktread_famread_ibdread_ibisread_mapread_plink2_king
Dependencies:bitbit64caclicliprclustercodetoolscolorspacecorrrcpp11crayondplyrevaluatefansifarverforeachgclusgenericsggplot2ggrepelgluegtablehighrhmsisobanditeratorskinship2knitrlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepermutepillarpkgconfigprettyunitsprogresspurrrqapquadprogR6RColorBrewerRcppreadrregistryrlangscalesseriationstringistringrtibbletidyrtidyselectTSPtzdbutf8vctrsveganviridisLitevroomwithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Order IDs across two columns | arrange_ids |
| Calculate Accuracy | calc_accuracy |
| Calculate various statistics from a confusion matrix | calc_stats |
| Calculate various statistics from a confusion matrix | confusion_matrix |
| Degree tibble | dibble |
| Fam to pedigree | fam2ped |
| Compute kinship coefficient from IBD segments | ibd2kin |
| Interpolate over segments | interpolate |
| Kinship coefficient to cM | kin2cm |
| Kinship coefficient to degree | kin2degree |
| Pedigree to pairwise kinship | ped2kinpair |
| Plot pedigree | plot_pedigree |
| Read AKT kin output file | read_akt |
| Read PLINK-formatted .fam file | read_fam |
| Read IBD segment file | read_ibd |
| Read IBIS coef output file | read_ibis |
| Read genetic map file | read_map |
| Read PLINK KING table | read_plink2_king |
