Risa: Converting experimental metadata from ISA-tab into Bioconductor data structures
Version 1.18.0

The Investigation / Study / Assay (ISA) tab-delimited format is a general purpose framework with which to collect and communicate complex metadata (i.e. sample characteristics, technologies used, type of measurements made) from experiments employing a combination of technologies, spanning from traditional approaches to high-throughput techniques. Risa allows to access metadata/data in ISA-Tab format and build Bioconductor data structures. Currently, data generated from microarray, flow cytometry and metabolomics-based (i.e. mass spectrometry) assays are supported. The package is extendable and efforts are undergoing to support metadata associated to proteomics assays.

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AuthorAlejandra Gonzalez-Beltran, Audrey Kauffmann, Steffen Neumann, Gabriella Rustici, ISA Team
Bioconductor views Annotation DataImport MassSpectrometry
Date of publicationNone
MaintainerAlejandra Gonzalez-Beltran <alejandra.gonzalez.beltran@gmail.com>
LicenseLGPL
Version1.18.0
URL http://www.isa-tools.org/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Risa")

Man pages

AssayTab-class: Class '"AssayTab"', a class for maintaing the information of...
getAnnotatedDataFrameAssay: Retrieves an AnnotatedDataFrameAssay.
getAssayRawDataFilenames-methods: ~~ Methods for Function 'getAssayRawDataFilenames' in Package...
getExpressionSet: Retrieves an ExpressionSet for a DNA microarray assay.
getMIAMEMetadata: Retrieves the MIAME information about a microarray experiment
getMicroarrayAssayFilenames: Listing filenames of microarray-based asssay from an ISAtab...
getMSAssayFilenames: Retrieves a vector with the assay filenames corresponding to...
getRawDataFilenames-methods: ~~ Methods for Function 'getRawDataFilenames' in Package...
getStudyFilename: Retrieves the study filename to which an assay.filename...
ISAtab-class: Class '"ISATab"', a class for maintaing ISATab information
isMicroarrayAssay: Determines if an assay is microarray-based or not.
isMSAssay: Indicates if an assay filename corresponds to a mass...
processAssayXcmsSet: Build an xcmsSet object given a mass spectrometry assay and...
processAssayXcmsSet.1factor: Build an xcmsSet object given a mass spectrometry assay and...
readISAtab: Reads an ISAtab dataset into an R object.
Risa-package: Risa package overview
suggestBiocPackage: Suggest Bioconductor pacakges
updateAssayMetadata: Update metadata into the assay file
write.assay.file: Write an Assay File from the ISA-Tab dataset
write.investigation.file: Writes the Investigation File of an ISA-Tab dataset
write.isatab: Write an ISA-Tab dataset
write.study.file: Write a Study File of an ISA-Tab dataset

Functions

AssayTab-class Man page
ISATab-class Man page
MSAssayTab-class Man page
MicroarrayAssayTab-class Man page
NMRAssayTab Man page
Risa Man page
Risa-package Man page
SeqAssayTab Man page
[,AssayTab,ANY,ANY,ANY-method Man page
[,AssayTab-method Man page
[,ISATab,ANY,ANY,ANY-method Man page
[,ISATab-method Man page
[<-,AssayTab,ANY,ANY,ANY-method Man page
[<-,AssayTab-method Man page
[<-,ISATab,ANY,ANY,ANY-method Man page
[<-,ISATab-method Man page
checkFilesExist Source code
getAnnotatedDataFrameAssay Man page Source code
getAssayRawDataFilenames Man page
getAssayRawDataFilenames,AssayTab,logical-method Man page
getAssayRawDataFilenames,MSAssayTab,logical-method Man page
getAssayRawDataFilenames,MicroarrayAssayTab,logical-method Man page
getAssayRawDataFilenames,NMRAssayTab,logical-method Man page
getAssayRawDataFilenames,SeqAssayTab,logical-method Man page
getAssayRawDataFilenames-methods Man page
getExpressionSet Man page Source code
getMIAMEMetadata Man page Source code
getMSAssayFilenames Man page Source code
getMicroarrayAssayFilenames Man page Source code
getMicroarrayDerivedDataFilenames Source code
getMicroarrayDerivedDataFilenamesAssay Source code
getPackagesInBiocView Source code
getRawDataFilenames Man page
getRawDataFilenames,ISATab,logical-method Man page
getRawDataFilenames-methods Man page
getStudyFilename Man page Source code
getStudyFilenameIndex Source code
isMSAssay Man page Source code
isMicroarrayAssay Man page Source code
processAssayXcmsSet Man page Source code
processAssayXcmsSet.1factor Man page Source code
readISAtab Man page Source code
readISAtabFiles Source code
readISAtabZip Source code
suggestBiocPackage Man page Source code
trim Source code
updateAssayMetadata Man page Source code
validMSAssayTabObject Source code
validMicroarrayAssayTabObject Source code
write.ISAtab Man page Source code
write.assay.file Man page Source code
write.investigation.file Man page Source code
write.study.file Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/Risa-biocViews.R
R/Risa-microarray.R
R/Risa-ms.R
R/Risa.R
README.md
TODO
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/Risa.R
inst/doc/Risa.Rnw
inst/doc/Risa.pdf
inst/extdata
inst/extdata/ARMSTRONG-S-3-metadata.zip
inst/extdata/ISA-BiocViews-mapping.csv
inst/extdata/faahKO-metadata.zip
man
man/AssayTab-class.Rd
man/ISAtab-class.Rd
man/Risa-package.Rd
man/getAnnotatedDataFrameAssay.Rd
man/getAssayRawDataFilenames-methods.Rd
man/getExpressionSet.Rd
man/getMIAMEMetadata.Rd
man/getMSAssayFilenames.Rd
man/getMicroarrayAssayFilenames.Rd
man/getRawDataFilenames-methods.Rd
man/getStudyFilename.Rd
man/isMSAssay.Rd
man/isMicroarrayAssay.Rd
man/processAssayXcmsSet.1factor.Rd
man/processAssayXcmsSet.Rd
man/readISAtab.Rd
man/suggestBiocPackage.Rd
man/updateAssayMetadata.Rd
man/write.assay.file.Rd
man/write.investigation.file.Rd
man/write.isatab.Rd
man/write.study.file.Rd
vignettes
vignettes/Risa.Rnw
Risa documentation built on May 20, 2017, 9:52 p.m.