Converting experimental metadata from ISA-tab into Bioconductor data structures


[Up] [Top]

Documentation for package ‘Risa’ version 1.10.0

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