Overview | Demonstration | Methodology review | Classes and Methods | Additional Case studies | Discussion | Session information
Package: OSAT 1.61.0
Li Yan
OSAT: OSAT: Optimal Sample Assignment Tool
A sizable genomics study such as microarray often involves the use of multiple batches (groups) of experiment due to practical complication. To minimize batch effects, a careful experiment design should ensure the even distribution of biological groups and confounding factors across batches. OSAT (Optimal Sample Assignment Tool) is developed to facilitate the allocation of collected samples to different batches. With minimum steps, it produces setup that optimizes the even distribution of samples in groups of biological interest into different batches, reducing the confounding or correlation between batches and the biological variables of interest. It can also optimize the even distribution of confounding factors across batches. Our tool can handle challenging instances where incomplete and unbalanced sample collections are involved as well as ideal balanced RCBD. OSAT provides a number of predefined layout for some of the most commonly used genomics platform. Related paper can be find at http://www.biomedcentral.com/1471-2164/13/689 .
Authors:
OSAT_1.61.0.tar.gz
OSAT_1.61.0.zip(r-4.7)OSAT_1.61.0.zip(r-4.6)OSAT_1.61.0.zip(r-4.5)
OSAT_1.61.0.tgz(r-4.6-any)OSAT_1.61.0.tgz(r-4.5-any)
OSAT_1.61.0.tar.gz(r-4.7-any)OSAT_1.61.0.tar.gz(r-4.6-any)
OSAT_1.61.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
OSAT/json (API)
| # Install 'OSAT' in R: |
| install.packages('OSAT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- BeadChip96ToMSA4MAP - Class '"MSAroboticPlate"'
- gc - R data object based on example file.
- GenotypingChip - Class '"BeadChip"'
- gs - R data object based on example file.
- gSetup - R data object based on example file.
- gSetup2 - R data object based on example file.
- IlluminaBeadChip - Class '"BeadChip"'
- IlluminaBeadChip24Plate - Class '"BeadPlate"'
- IlluminaBeadChip48Plate - Class '"BeadPlate"'
- IlluminaBeadChip96Plate - Class '"BeadPlate"'
- MSA4.plate - Class '"MSAroboticPlate"'
- pheno - R data object based on example file.
On BioConductor:OSAT-1.61.0(bioc 3.24)OSAT-1.60.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
datarepresentationvisualizationexperimentaldesignqualitycontrol
Last updated from:2ca42305a2. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 286 | ||
| linux-devel-x86_64 | NOTE | 124 | ||
| source / vignettes | OK | 237 | ||
| linux-release-x86_64 | NOTE | 159 | ||
| macos-release-arm64 | NOTE | 81 | ||
| macos-oldrel-arm64 | NOTE | 117 | ||
| windows-devel | NOTE | 90 | ||
| windows-release | NOTE | 78 | ||
| windows-oldrel | NOTE | 67 | ||
| wasm-release | OK | 100 |
Exports:BeadChip96ToMSA4MAPcreate.experiment.setupcreate.optimized.setupexclude<-GenotypingChipget.experiment.setupgetLayoutIlluminaBeadChipIlluminaBeadChip24PlateIlluminaBeadChip48PlateIlluminaBeadChip96Plateinitializemap.to.MSAmetadatametadata<-MSA4.platemulti.barplotmulti.chisq.testoptimal.blockoptimal.shuffleplotpredefinedQCsetup.containersetup.sampleshowsummary
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Class '"BeadChip"' | BeadChip-class GenotypingChip getLayout,BeadChip-method IlluminaBeadChip |
| Class '"BeadPlate"' | BeadPlate-class IlluminaBeadChip24Plate IlluminaBeadChip48Plate IlluminaBeadChip96Plate |
| Create optimized setup | create.optimized.setup |
| R data object based on example file. | gc gs gSetup gSetup2 pheno |
| Class '"gArray"' | dim,gArray-method gArray-class getLayout getLayout,gArray-method metadata metadata,gArray-method metadata<- metadata<-,gArray-method ncol,gArray-method nrow,gArray-method |
| Class '"gAssembly"' | gAssembly-class getLayout,gAssembly-method initialize,gAssembly-method metadata,gAssembly-method metadata<-,gAssembly-method show,gAssembly-method |
| Class '"gContainer"' | cid,gContainer-method exclude<- exclude<-,gContainer-method gContainer-class get.gAssembly,gContainer-method getLayout,gContainer-method initialize,gContainer-method metadata,gContainer-method metadata<-,gContainer-method setup.container show,gContainer-method |
| Get experiment assignment after optimization. | get.experiment.setup |
| Class '"gExperimentSetup"' | create.experiment.setup get.gAssembly,gExperimentSetup-method gExperimentSetup-class initialize,gExperimentSetup-method metadata,gExperimentSetup-method metadata<-,gExperimentSetup-method samples,gExperimentSetup-method show,gExperimentSetup-method summary,gExperimentSetup-method |
| Class '"gPlate"' | getLayout, gPlate-method gPlate-class initialize,gPlate-method show,gPlate-method |
| Class 'gSample' | gSample-class initialize,gSample-method setup.sample show,gSample-method summary summary,gSample-method |
| Class '"gSlide"' | getLayout,gSlide-method gSlide-class initialize,gSlide-method show,gSlide-method |
| Class '"MSAroboticPlate"' | BeadChip96ToMSA4MAP getLayout,MSAroboticPlate-method initialize,MSAroboticPlate-method map.to.MSA map.to.MSA,data.frame,MSAroboticPlate-method map.to.MSA,gExperimentSetup,MSAroboticPlate-method MSA4.plate MSAroboticPlate-class show,MSAroboticPlate-method |
| multi.barplot | multi.barplot |
| multi.chisq.test | multi.chisq.test |
| optimal.block | optimal.block |
| optimal.shuffle | optimal.shuffle |
| Methods for Function 'plot' | plot,gExperimentSetup,missing-method plot-methods |
| Show predefined objects in the package. | predefined |
| QC | QC |
