# Converting experimental metadata from ISA-tab into Bioconductor data structures

## Documentation for package ‘Risa’ version 1.8.0

- 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