# Implementation for the ISA Abstract Model

## Documentation for package ‘isatabr’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

aFiles | Get and set aFiles.
aFiles-method | Get and set aFiles.
aFiles<- | Get and set aFiles.
aFiles<--method | Get and set aFiles.
assayTab | S4 Class assayTab, initialization methods
assayTab-class | S4 Class assayTab, initialization methods
getAssayFileNames | Retrieve the Assay File Name(s) per Study from an ISA object.
getAssayTabs | Retrieve Assay Tables from an ISA object.
getStudyFileNames | Retrieve the Study Identifier(s) and Study File Name(s) from an ISA object.
iContacts | Get and set iContacts.
iContacts-method | Get and set iContacts.
iContacts<- | Get and set iContacts.
iContacts<--method | Get and set iContacts.
iFileName | Get and set iFileName
iFileName-method | Get and set iFileName
iFileName<- | Get and set iFileName
iFileName<--method | Get and set iFileName
initialize-method | S4 Class ISA, initialization method
invest | Get and set invest.
invest-method | Get and set invest.
invest<- | Get and set invest.
invest<--method | Get and set invest.
iPubs | Get and set iPubs.
iPubs-method | Get and set iPubs.
iPubs<- | Get and set iPubs.
iPubs<--method | Get and set iPubs.
ISA | S4 Class ISA, initialization method
ISA-class | S4 Class ISA, initialization method
ISA-initialize | S4 Class ISA, initialization method
isaPath | Get and set path
isaPath-method | Get and set path
isaPath<- | Get and set path
isaPath<--method | Get and set path
microarrayAssayTab | S4 Class assayTab, initialization methods
microarrayAssayTab-class | S4 Class assayTab, initialization methods
msAssayTab | S4 Class assayTab, initialization methods
msAssayTab-class | S4 Class assayTab, initialization methods
oSR | Get and set oSR
oSR-method | Get and set oSR
oSR<- | Get and set oSR
oSR<--method | Get and set oSR
processAssay | Process assay tab data
processAssay-method | Process assay tab data
readISATab | Read an ISA-Tab dataset into an R object.
sAssays | Get and set sAssays.
sAssays-method | Get and set sAssays.
sAssays<- | Get and set sAssays.
sAssays<--method | Get and set sAssays.
sContacts | Get and set sContacts.
sContacts-method | Get and set sContacts.
sContacts<- | Get and set sContacts.
sContacts<--method | Get and set sContacts.
sDD | Get and set sDD.
sDD-method | Get and set sDD.
sDD<- | Get and set sDD.
sDD<--method | Get and set sDD.
sFacts | Get and set sFacts.
sFacts-method | Get and set sFacts.
sFacts<- | Get and set sFacts.
sFacts<--method | Get and set sFacts.
sFiles | Get and set sFiles.
sFiles-method | Get and set sFiles.
sFiles<- | Get and set sFiles.
sFiles<--method | Get and set sFiles.
sProts | Get and set sProts.
sProts-method | Get and set sProts.
sProts<- | Get and set sProts.
sProts<--method | Get and set sProts.
sPubs | Get and set sPubs.
sPubs-method | Get and set sPubs.
sPubs<- | Get and set sPubs.
sPubs<--method | Get and set sPubs.
study | Get and set study.
study-method | Get and set study.
study<- | Get and set study.
study<--method | Get and set study.
validISAObject | Check the validity of an object of class ISA.
writeAssayFiles | Write ISA-Tab object.
writeInvestigationFile | Write ISA-Tab object.
writeISAtab | Write ISA-Tab object.
writeStudyFiles | Write ISA-Tab object.