Package: isatabr 1.0.1.9000
Bart-Jan van Rossum
isatabr: Implementation for the ISA Abstract Model
ISA is a metadata framework to manage an increasingly diverse set of life science, environmental and biomedical experiments. In isatabr methods for reading, modifying and writing of files in the ISA-Tab format are implemented. It also contains methods for processing assay data.
Authors:
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isatabr.pdf |isatabr.html✨
isatabr/json (API)
NEWS
| # Install 'isatabr' in R: |
| install.packages('isatabr', repos = c('https://biometris.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/biometris/isatabr/issues
Last updated 1 years agofrom:1a17b87454. Checks:OK: 6 NOTE: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 17 2024 |
| R-4.5-win | OK | Nov 17 2024 |
| R-4.5-linux | OK | Nov 17 2024 |
| R-4.4-win | OK | Nov 17 2024 |
| R-4.4-mac | OK | Nov 17 2024 |
| R-4.3-win | OK | Nov 17 2024 |
| R-4.3-mac | NOTE | Nov 17 2024 |
Exports:aFilesaFiles<-getAssayFileNamesgetAssayTabsgetStudyFileNamesiContactsiContacts<-iFileNameiFileName<-initializeinvestinvest<-iPubsiPubs<-isaPathisaPath<-oSRoSR<-processAssayreadISATabsAssayssAssays<-sContactssContacts<-sDDsDD<-sFactssFacts<-sFilessFiles<-sProtssProts<-sPubssPubs<-studystudy<-validISAObjectwriteAssayFileswriteInvestigationFilewriteISAtabwriteStudyFiles
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get and set aFiles. | aFiles aFiles,ISA-method aFiles<- aFiles<-,ISA-method |
| S4 Class assayTab, initialization methods | assayTab assayTab-class microarrayAssayTab microarrayAssayTab-class msAssayTab msAssayTab-class |
| Retrieve the Assay File Name(s) per Study from an ISA object. | getAssayFileNames |
| Retrieve Assay Tables from an ISA object. | getAssayTabs |
| Retrieve the Study Identifier(s) and Study File Name(s) from an ISA object. | getStudyFileNames |
| Get and set iContacts. | iContacts iContacts,ISA-method iContacts<- iContacts<-,ISA-method |
| Get and set iFileName | iFileName iFileName,ISA-method iFileName<- iFileName<-,ISA-method |
| Get and set invest. | invest invest,ISA-method invest<- invest<-,ISA-method |
| Get and set iPubs. | iPubs iPubs,ISA-method iPubs<- iPubs<-,ISA-method |
| S4 Class ISA, initialization method | initialize,ISA-method ISA ISA-class ISA-initialize |
| Get and set path | isaPath isaPath,ISA-method isaPath<- isaPath<-,ISA-method |
| Get and set oSR | oSR oSR,ISA-method oSR<- oSR<-,ISA-method |
| Process assay tab data | processAssay processAssay,ISA,assayTab,character-method processAssay,ISA,assayTab-method processAssay,ISA,microarrayAssayTab,character-method processAssay,ISA,msAssayTab,character-method processAssay,ISA,msAssayTab-method |
| Read an ISA-Tab dataset into an R object. | readISATab |
| Get and set sAssays. | sAssays sAssays,ISA-method sAssays<- sAssays<-,ISA-method |
| Get and set sContacts. | sContacts sContacts,ISA-method sContacts<- sContacts<-,ISA-method |
| Get and set sDD. | sDD sDD,ISA-method sDD<- sDD<-,ISA-method |
| Get and set sFacts. | sFacts sFacts,ISA-method sFacts<- sFacts<-,ISA-method |
| Get and set sFiles. | sFiles sFiles,ISA-method sFiles<- sFiles<-,ISA-method |
| Get and set sProts. | sProts sProts,ISA-method sProts<- sProts<-,ISA-method |
| Get and set sPubs. | sPubs sPubs,ISA-method sPubs<- sPubs<-,ISA-method |
| Get and set study. | study study,ISA-method study<- study<-,ISA-method |
| Check the validity of an object of class ISA. | validISAObject |
| Write ISA-Tab object. | writeAssayFiles writeInvestigationFile writeISAtab writeStudyFiles |
