CHANGES IN VERSION 2.2.0
-------------------------

BUG FIXES

    o Fix import exprs<- bug in loadMAdata.

CHANGES IN VERSION 2.0.1
-------------------------

BUG FIXES

    o Fix error message handling in network plot in exploreGSAres().

CHANGES IN VERSION 2.0.0
-------------------------

NEW FEATURES

    o Added a function exploreGSAres() for interactively exploring the result object
      returned by runGSA(). This opens a Shiny app in a browser where users can view
      the different results tables and figures and get detailed information on specific
      gene-sets and genes.

    o Added a function networkPlot2() that is an improvement to the old function
      networkPlot().

DOCUMENTATION

        o Added a new vignette focused on gene-set analysis

CHANGES IN VERSION 1.22.0
-------------------------

DOCUMENTATION

    o Update installation instructions in the vignette

CHANGES IN VERSION 1.20.1
-------------------------

DOCUMENTATION

    o Updates to GitHub landing page (README.md)

CHANGES IN VERSION 1.18.1
-------------------------

BUG FIXES

    o Fix parsing of gmt files when gene-set name contains spaces

CHANGES IN VERSION 1.18.0
-------------------------

DOCUMENTATION

    o Switched to accommodate documentation in r-files using roxygen

BUG FIXES

    o Fix print addInfo for GSC bug

CHANGES IN VERSION 1.16.4
-------------------------

BUG FIXES

    o  Fix R CMD check NOTE on calling require(snowfall)

CHANGES IN VERSION 1.16.3
-------------------------

BUG FIXES

    o Fix BiocGenerics::sd and stats::sd collision when loading

CHANGES IN VERSION 1.16.2
-------------------------

BUG FIXES

    o Fix error: "Error in if (maxP > -minP) { : missing value where TRUE/FALSE needed"
      that appeared occasionally during runGSA for method gsea. This happened when the
      running sum was only positive or only negative, leading to that the if-statement
      broke due to missing values.

CHANGES IN VERSION 1.16.1
-------------------------

BUG FIXES

    o Fix biomaRt Rchunk in vignette to avoid build error

CHANGES IN VERSION 1.14.5
-------------------------

BUG FIXES

    o Reset plot layout after networkPlot.

    o Issue warning instead of error in writeFilesForKiwi when gene-level statistics
      are not p-values. This means that the GLS file will not be generated, but the
      GSS and GSC files are.

CHANGES IN VERSION 1.14.3
-------------------------

BUG FIXES

    o Required functions from the snow package, used by snowfall, are now properly loaded.

CHANGES IN VERSION 1.14
-----------------------

NEW FEATURES

    o Added new GSA method fgsea (fast GSEA) from the fgsea package.

    o Added max method as an option in consensusScores().

IMPROVEMENTS [credits to Alexey Sergushichev]

    o Updated the p-value calculation (while using gene permutation) from:
         sum(background >= value) / length(background)
      to:
         (sum(background >= value) + 1) / (length(background) + 1)
      where bakground is a vector of permuted gene-set statistics and value
      is the actual calculated gene-set statistic. This change avoids returning
      p-values = 0, instead the theoretically smallest possible p-value will be
      determined by the number of permutations used. E.g. for nPerm = 10000,
      the smallest p-value will be 1 / 10001 = 9.999e-05.

    o Improved speed of checkLoadArg().

    o Improved speed of gene-set statistic calculation for GSEA in calcGeneSetStat().

    o Improved speed of FDR calculation for GSEA in fdrGSEA().

BUG FIXES

    o Updated NAMESPACE to load dependencies in a better way.

    o Updated the parsing of sbml files in loadGSC().

    o Updated networkPlot() to conform to changes in the igraph package.

CHANGES IN VERSION 1.12
-----------------------
    o No changes

CHANGES IN VERSION 1.10.2
-------------------------

DOCUMENTATION

    o Updated the vignette R code to avoid an error in the call to biomart
	    throught the getBM function.

CHANGES IN VERSION 1.10.1
-------------------------

BUG FIXES

    o Fixed a bug in runGSA which returned wrong numbers for the up- and down-
	    regulated genes, for the GSEA method.

CHANGES IN VERSION 1.8.2
-------------------------

BUG FIXES

    o Updated loading of suggested packages from using require() to requireNamespace()
      instead.

CHANGES IN VERSION 1.6.2
-------------------------

BUG FIXES

    o Fixed a bug in loadMAdata so that normalizing using MAS5 is now returning
      log2-transformed expression values.

CHANGES IN VERSION 1.6.1
-------------------------

DOCUMENTATION

    o Updated this NEWS file

CHANGES IN VERSION 1.6.0
-------------------------

NEW FEATURES

    o Added a function writeFilesForKiwi() that enables a seamless integration of the
      output from a gene set analysis with piano to the network-based visualization
      offered by the python tool Kiwi.

CHANGES IN VERSION 1.4.2
-------------------------

BUG FIXES

    o Fixed a bug in loadMAdata so that mas5 can now be used for normalization.

CHANGES IN VERSION 1.4.1
-------------------------

BUG FIXES

    o Fixed a bug in GSAsummaryTable which returned an error in the case of analyzing
      only a single gene set.

CHANGES IN VERSION 1.4.0
-------------------------

NEW FEATURES

    o Added argument plot to consensusHeatmap() so that drawing the heatmap can
      be suppressed but the corresponding numerical matrix can be saved.

    o Added argument cellnote to consensusHeatmap() so that the information inside
      each cell of the heatmap can be chosen to be either the consensus scores (as
      previously), the median p-values, the number of genes or empty.

    o Added a matrix nGenesMat to the output of consensusHeatmap() containing the
      same information as printed in the heatmap if argument cellnote="nGenes".

    o Added arguments columnnames, colorkey, colorgrad and cex to consensusHeatmap()
      for better control of the column labels, toggling of the colorkey, color
      selection and text size.

    o Introduced the new function GSAheatmap(), which is similar to consensusHeatmap()
      but for only a single gene set result (gsaRes object).

BUG FIXES

    o Fixed a bug which for some settings of runGSA would not output number of up-
      and downregulated genes in the gene sets.

DOCUMENTATION

    o Updated consensusHeatmap() man page according to new changes in the function.

    o Added man page for GSAheatmap().

CHANGES IN VERSION 1.2.12
-------------------------

DOCUMENTATION

    o Updated the biocViews field in the DESCRIPTION file.

CHANGES IN VERSION 1.2.11
-------------------------

BUG FIXES

    o Fixed a typo in the code which made it impossible to execute runGSA successfully
      with the option sample permutation.

CHANGES IN VERSION 1.2.10
-------------------------

BUG FIXES

    o Fixed a bug in diffExp() that caused an error due to incorrect collection of the
      venn diagram gene members when only using one contrast/comparison.

CHANGES IN VERSION 1.2.9
-------------------------

BUG FIXES

    o Fixed a bug in consensusHetmap() so that the adjusted p-values are actually used
      if adjusted=TRUE.

CHANGES IN VERSION 1.2.8
-------------------------

BUG FIXES

    o Fixed bug in diffExp() that in rare cases failed to output the vennMembers.

CHANGES IN VERSION 1.2.7
-------------------------

BUG FIXES

    o Changed so that argument cutoff in consensusHeatmap() can be set to an arbitrarily
      high number (e.g. Inf) to easily include all gene sets.

CHANGES IN VERSION 1.2.6
-------------------------

BUG FIXES

    o Fixed bug in loadMAdata() that removed duplicate entries in the annotation in
      an incorrect way.

CHANGES IN VERSION 1.2.5
-------------------------

BUG FIXES

    o Fixed bug in diffExp() that returned incorrect gene IDs for $pValues and
      $foldChanges if and only if annotation was previously supplied to loadMAdata()
      AND the probeset IDs in the normalized data ($dataNorm) were unsorted. The
      $resTable is unnaffected.

CHANGES IN VERSION 1.2.4
-------------------------

BUG FIXES

    o Fixed bug in the volcano plot in diffExp() for coloring points black.

CHANGES IN VERSION 1.2.3
-------------------------

BUG FIXES

    o Improved error checking of supplied annotation in loadMAdata().

    o Improved error checking of chromosome mapping in polarPlot().

    o Fixed typo in loadMAdata man page.

CHANGES IN VERSION 1.2.2
-------------------------

DOCUMENTATION

    o Updated installation instructions in the vignette.

    o Fixed typo in consensusHeatmap man page.

CHANGES IN VERSION 1.2.1
-------------------------

BUG FIXES

    o Fixed bug in networkPlot() which gave an incorrect error message when gene
      set nodes were selected but no edges could be drawn. Now a correct error
      message is given.

CHANGES IN VERSION 1.2.0
-------------------------

NEW FEATURES

    o Added argument ncpus to runGSA(). Enables parts of this function to run in
      parallel, thus decreasing runtime. Requires R package snowfall.

    o Added function runGSAhyper() to perform gene set analysis using Fisher's exact test,
      as an alternative to runGSA.

    o Added information about genes in each area of the Venn diagram in the output
      of diffExp().

    o Added volcano plot as optional output of diffExp() and added argument volcanoFC.

    o Added argument ncharLabel to networkPlot() and consensusHeatmap() to control the
      length of the labels in the plots and add the option to not truncate them.

    o Added the yeast metabolic model iTO977 to be loaded with loadGSC(), for detecting
      reporter metabolites using gene set analysis. (See vignette.)

    o Added support for running networkPlot() on objects returned by runGSAhyper().

DOCUMENTATION

    o Minor updates to the vignette.

    o Updated diffExp() man page.

    o Restructered this NEWS file.

BUG FIXES

    o Updated diffExp() to handle changes in lmFit() and topTable() from limma.

    o Removed suppressWarnings(), as temporarily introduced in version 1.0.1, in
      polarPlot() around the calls to radial.plot() since warnings are now fixed in
      package plotrix.

    o Updated the main legend of the plot from consensusScores() to make it clearer.

    o Updated error-messages in networkPlot().

    o Fixed typo in PC variance plot produced by runQC().

CHANGES IN VERSION 1.0.7
-------------------------

DOCUMENTATION

    o Updated consensusScores() man page.

CHANGES IN VERSION 1.0.6
-------------------------

DOCUMENTATION

    o Updated loadMAdata() man page.

CHANGES IN VERSION 1.0.5
-------------------------

BUG FIXES

    o Updated diffExp() to only use vennDiagram() of the limma package for Venn
      diagram plotting in order to correct a bug when plotting more than three
      circles. Also updated the corresponding man page.

DOCUMENTATION

    o Updated the SBML section in the loadGSC() man page.

CHANGES IN VERSION 1.0.4
-------------------------

BUG FIXES

    o Fixed bug in loadMAdata so that also compressed CEL-files (*.CEL.gz) can be
      loaded correctly.

CHANGES IN VERSION 1.0.3
-------------------------

DOCUMENTATION

    o Updated references in vignette.

CHANGES IN VERSION 1.0.2
-------------------------

DOCUMENTATION

    o Updated CITATION information.


CHANGES IN VERSION 1.0.1
-------------------------

DOCUMENTATION

    o Updated CITATION information.

    o Fixed typos in DESCRIPTION and piano-package.Rd.

    o Updated the man file for loadGSC().

    o Added URL in DESCRIPTION.

BUG FIXES

    o Fixed bug in loadGSC() so that gmt-files are now loaded correctly.

    o Temporarily added suppressWarnings() in polarPlot() around the calls to
      radial.plot() since warnings appeared for example("radial.plot") in
      plotrix v3.4-6.

CHANGES IN VERSION 1.0.0
-------------------------

NEW FEATURES

    o Now part of Bioconductor.

    o Removed the arguments 'venn', 'heatmap' and 'polarPlot' from diffExp and
      replaced them with a new argument: 'plot'.

    o The consensusScores function now does not return its result invisibly.

    o The argument order in consensusScores has changed: 'plot' has been moved
      from last place to after 'method'.

    o Removed contrastName as output from runGSA and geneSetSummary, including
      man pages.

    o Changed name of folder for example data from exampleData to extdata, and
      updated man pages and vignette.

    o Changed so that total number of gene-level statistics are printed during
      run, instead of total number of unique genes.

DOCUMENTATION

    o Added citation DOI to vignette.

    o Updated the man page for consensusScores, added correct output description.

    o Updated the Description field text in the DESCRIPTION file.

    o Changed the man page for consensusHeatmap clarifying that the cutoff
      argument is consensus score (not rank)

    o Updated the man page for loadGSC, clarifying the input.

    o Reworked the vignette to fit Bioconductor, removed section on R
      introduction.

    o Removed 'typical usages' section from man page of loadMAdata since this
      is covered in the vignette.

    o Updated the examples for diffExp, networkPlot, consensusHeatmap and
      consensusScores to show how to handle the returned object.

    o Added CITATION file.

    o Added NEWS file.

    o Added more links to similar packages in runGSA help page.

    o Updated the installation instructions in the Vignette to fit Bioconductor.

BUG FIXES

    o Fixed bug in geneSetSummary when no directions are available.

    o Fixed a bug in diffExp() regarding the result table, when gene names
      (annotation) are not available

    o Fixed a bug in diffExp() so that the heatmap shows gene names if available,
      otherwise the probeset IDs

    o Removed man page for internal functions.

    o Updated the loadMAdata function to use the justPlier function from package
      plier, instead of a modified version.

    o Removed internal function justPlierSpec.
