Package: pbatR 2.2-17
Thomas Hoffmann
pbatR: Pedigree/Family-Based Genetic Association Tests Analysis and Power
This R package provides power calculations via internal simulation methods. The package also provides a frontend to the now abandoned PBAT program (developed by Christoph Lange), and reads in the corresponding output and displays results and figures when appropriate. The license of this R package itself is GPL. However, to have the program interact with the PBAT program for some functionality of the R package, users must additionally obtain the PBAT program from Christoph Lange, and accept his license. Both the data analysis and power calculations have command line and graphical interfaces using tcltk.
Authors:
pbatR_2.2-17.tar.gz
pbatR_2.2-17.tar.gz(r-4.5-noble)pbatR_2.2-17.tar.gz(r-4.4-noble)
pbatR_2.2-17.tgz(r-4.4-emscripten)pbatR_2.2-17.tgz(r-4.3-emscripten)
pbatR.pdf |pbatR.html✨
pbatR/json (API)
| # Install 'pbatR' in R: |
| install.packages('pbatR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 8 months agofrom:239ee59536. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 27 2024 |
| R-4.5-linux-x86_64 | OK | Aug 27 2024 |
Exports:affectionPheas.cpedas.pedas.pedlistas.pheas.ppedc2batfread.cpedfread.pedfread.pheis.cpedis.finishedis.pedis.pedlistis.pheis.ppedobfuscatepbatpbat.cleanpbat.concatenatepbat.create.commandfilepbat.filespbat.firsttimepbat.getpbat.getmodepbat.getwinepbat.helppbat.lastpbat.last.rawResultspbat.loadpbat.mpbat.objpbat.powerpbat.powerCmdpbat.setpbat.setmodepbat.setmode.defaultspbat.setVersionCheckpbat.setwinepbat.statuspbat.unworkpbat.workpedMarkerNamesplotCPedplotPedread.cpedread.pedread.pheread.ppedtopwrite.cpedwrite.pbatwrite.pbat.csvwrite.pedwrite.phe
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Affection Phenotype Object | affectionPhe |
| C2BAT | c2bat |
| Cleaning pbat(), pbat.last(), pbat.m() output. | pbat.clean |
| Cluster result functions | is.finished pbat.concatenate pbat.load |
| Phenotype Object | as.cped fread.cped is.cped plotCPed read.cped sort.cped write.cped |
| `pbat' Object Generic Routines | plot.pbat print.pbat summary.pbat |
| Obfuscating Pedigree and Phenotype Files | obfuscate |
| PBAT Graphical and Command Line Interface | pbat pbat.create.commandfile pbat.files pbat.last pbat.last.rawResults pbat.m pbat.obj |
| Help and Reporting Information | pbat.firsttime pbat.help |
| Set Pbat Parameters | pbat.get pbat.getmode pbat.getwine pbat.set pbat.setmode pbat.setmode.defaults pbat.setVersionCheck pbat.setwine |
| PBAT Status of Run | pbat.status |
| pbatRwork Temp Directory | pbat.unwork pbat.work |
| Pedigree Object | as.ped as.pedlist as.pped fread.ped is.ped is.pedlist is.pped pedMarkerNames plotPed read.ped read.pped sort.ped write.ped |
| Phenotype Object | as.phe fread.phe is.phe read.phe sort.phe write.phe |
| Power Exploration | pbat.power pbat.powerCmd |
| top | top |
| Saving `pbat' Object | write.pbat write.pbat.csv |