Converting experimental metadata from ISA-tab into Bioconductor data structures

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Documentation for package ‘Risa’ version 1.42.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

Risa-package	Risa package overview
AssayTab-class	Class '"AssayTab"', a class for maintaing the information of AssayTab
getAnnotatedDataFrameAssay	Retrieves an AnnotatedDataFrameAssay.
getAssayRawDataFilenames	~~ Methods for Function 'getAssayRawDataFilenames' in Package 'Risa' ~~
getAssayRawDataFilenames-method	~~ Methods for Function 'getAssayRawDataFilenames' in Package 'Risa' ~~
getAssayRawDataFilenames-methods	~~ Methods for Function 'getAssayRawDataFilenames' in Package 'Risa' ~~
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 dataset.
getMSAssayFilenames	Retrieves a vector with the assay filenames corresponding to mass spectrometry.
getRawDataFilenames	~~ Methods for Function 'getRawDataFilenames' in Package 'Risa' ~~
getRawDataFilenames-method	~~ Methods for Function 'getRawDataFilenames' in Package 'Risa' ~~
getRawDataFilenames-methods	~~ Methods for Function 'getRawDataFilenames' in Package 'Risa' ~~
getStudyFilename	Retrieves the study filename to which an assay.filename corresponds.
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 spectrometry assay.
MicroarrayAssayTab-class	Class '"AssayTab"', a class for maintaing the information of AssayTab
MSAssayTab-class	Class '"AssayTab"', a class for maintaing the information of AssayTab
NMRAssayTab	Class '"AssayTab"', a class for maintaing the information of AssayTab
processAssayXcmsSet	Build an xcmsSet object given a mass spectrometry assay and considering all factors defined
processAssayXcmsSet.1factor	Build an xcmsSet object given a mass spectrometry assay and considering the first factor defined
readISAtab	Reads an ISAtab dataset into an R object.
Risa	Risa package overview
SeqAssayTab	Class '"AssayTab"', a class for maintaing the information of AssayTab
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
[-method	Class '"AssayTab"', a class for maintaing the information of AssayTab
[-method	Class '"ISATab"', a class for maintaing ISATab information
[<--method	Class '"AssayTab"', a class for maintaing the information of AssayTab
[<--method	Class '"ISATab"', a class for maintaing ISATab information