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

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.

AuthorAlejandra Gonzalez-Beltran, Audrey Kauffmann, Steffen Neumann, Gabriella Rustici, ISA Team
Date of publicationNone
MaintainerAlejandra Gonzalez-Beltran <alejandra.gonzalez.beltran@gmail.com>

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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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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