Moved ms methods to new file, added methods for factors and groups
Added factors as an slot in the ISAtab class
Added definition of treatments and modified definition of factors to work for multiple study files
Added definition of groups
Fixed treatments and groups definitions to work for multiple study files
Added assay.names as another slot in the ISAtab-class
Changed processAssayXcmsSet methods, eliminating for loop, added new term for isatab.syntax
The method processAssayXcmsSet now uses all the factors to build the sclass object, instead of just the first one #12
Fixed definition of factors/treatments/groups for a single study/single factor investigation
Validations for setFactors, setTreatments, setGroups, verbose also used for readISAtab method
Fixed variable name
Changed NEWS.Rd to NEWS, added NEWS for this version, added documentation, added isatab.syntax to the NAMESPACE
Added getRawDataFiles method for mass spectrometry experiments
Added initial version methods biocViews
Implemented suggestBiocPackage and reorganised NAMESPACE
Fixed definitions of treatments and groups for composite datasets
Changed added biocViews to Depends, added version parameter to suggestBiocPackage
Bumped version number to devel, added getMSASsayFilenames to NAMESPACE, fixed getRawDataFiles to work for ISAtab datasets containing non-ms assays, added documentation
Extended the package documentation
Added documentation for new methods