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:Bart-Jan van Rossum [aut, cre], Maikel Verouden [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
isatabr/json (API)

# 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

On CRAN:

isa isatab

3.70 score 3 scripts 206 downloads 41 exports 0 dependencies

Last updated from:1a17b87454. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	184
source / vignettes	OK	242
linux-release-x86_64	OK	187
macos-release-arm64	OK	107
macos-oldrel-arm64	OK	194
windows-devel	OK	123
windows-release	OK	136
windows-oldrel	OK	137
wasm-release	OK	141

Exports:aFiles aFiles<-getAssayFileNames getAssayTabs getStudyFileNames iContacts iContacts<-iFileName iFileName<-initialize invest invest<-iPubs iPubs<-isaPath isaPath<-oSR oSR<-processAssay readISATab sAssays sAssays<-sContacts sContacts<-sDD sDD<-sFacts sFacts<-sFiles sFiles<-sProts sProts<-sPubs sPubs<-study study<-validISAObject writeAssayFiles writeInvestigationFile writeISAtab writeStudyFiles

Dependencies:

An introduction to the isatabr package

Rendered fromisatabr.Rmdusingknitr::rmarkdown

Last update: 2021-07-14
Started: 2021-06-18

Citation

Development and contributors

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