Function reference • isatabr

Read ISA-Tab files

readISATab(): Read an ISA-Tab dataset into an R object.

validISAObject(): Check the validity of an object of class ISA.

initialize(<ISA>): S4 Class ISA, initialization method

Get and set ISA object slots

isaPath() `isaPath<-`(): Get and set path

iFileName() `iFileName<-`(): Get and set iFileName

oSR() `oSR<-`(): Get and set oSR

invest() `invest<-`(): Get and set invest.

iPubs() `iPubs<-`(): Get and set iPubs.

iContacts() `iContacts<-`(): Get and set iContacts.

study() `study<-`(): Get and set study.

sDD() `sDD<-`(): Get and set sDD.

sPubs() `sPubs<-`(): Get and set sPubs.

sFacts() `sFacts<-`(): Get and set sFacts.

sAssays() `sAssays<-`(): Get and set sAssays.

sProts() `sProts<-`(): Get and set sProts.

sContacts() `sContacts<-`(): Get and set sContacts.

sFiles() `sFiles<-`(): Get and set sFiles.

aFiles() `aFiles<-`(): Get and set aFiles.

Write ISA-Tab files

writeISAtab() writeInvestigationFile() writeStudyFiles() writeAssayFiles(): Write ISA-Tab object.

Process assay data

getAssayTabs(): Retrieve Assay Tables from an ISA object.

assayTab-class assayTab msAssayTab-class msAssayTab microarrayAssayTab-class microarrayAssayTab: S4 Class assayTab, initialization methods

processAssay(): Process assay tab data

Convenience functions

getStudyFileNames(): Retrieve the Study Identifier(s) and Study File Name(s) from an ISA object.

getAssayFileNames(): Retrieve the Assay File Name(s) per Study from an ISA object.