Package index • isajsonr

Read ISA-JSON files

readISAJSON(): Read an ISA-JSON file into an R object.

validISAJSONObject(): Check the validity of an object of class ISAjson.

ISAjson-class ISAjson: S4 Class ISAjson, initialization method

initialize(<ISAjson>): Constructor method of ISAjson-class.

Get and set ISA object sections

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

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.

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

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

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

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

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

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

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

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

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

Write ISA-JSON files

writeISAjson(): Write ISA-JSON object.

Process assay data

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

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

processAssay(): Process assay tab data

processAllAssays(): Process all assay tab data

Convenience functions

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

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