NEWS for Risa package

Changes for 1.3.3
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1. Fixed definitions of assay.filenames.per.sample and factors.
2. Fixed regulession of investigation file (i_) to be considered at the beginning of the string. 
3. Added CITATION file.

Changes for 1.1.0
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1. The ISAtab-class was extended to include the definition of assay.names, factors, treatments and groups.
2. The previous processAssayXcmsSet method was split into processAssayXcmsSet.1factor and processAssayXcmsSet to consider the first factor only (as it was in the previous definition) or all the factors, respectively.
3. More methods for processing mass spectrometry assays were added:
  - the method getMSAssayFilenames retrieves a list with the mass spectrometry assay filenames 
  - the method getRawDataFiles retrieves a list with all the files listed under the column 'Raw Spectral Data File' within the mass spectrometry assays.
  - the method is.ms receives an object from the ISAtab-class and an assay filename as parameter, and retrieves TRUE if the assay filename is a mass spectrometry assay, or FALSE otherwise.
4. A method called suggestBiocPackage was added, which retrieves a list of packages in Bioconductor that might be relevant to the ISAtab dataset, according to its assays' mesaurement and technology types. This method relies on the BiocViews annotations for each of the packages available in Bioconductor in a specific version.
5. Added AssayTab-class and subclasses for MS, Microarray, Seq and NMR.
6. Defined method getAssayRawDataFilenames and getRawDataFilenames
7. Defined method getExpressionSet for microarray assays relying on affy package.

Changes for 1.0.0
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This is the first release version of the package. It contains functionality to parse ISAtab datasets into an R object from the ISAtab class. It also provides functionality to save the ISA-tab dataset, or each of its individual files. Additionally, it is also possible to update assay files. Currently, metadata associated to proteomics and metabolomics-based assays (i.e. mass spectrometry) can be processed into an xcmsSet object (from the xcms R package).