NEWS

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piano 2.2.0

BUG FIXES

• Fix import exprs<- bug in loadMAdata.

piano 2.0.1

BUG FIXES

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

piano 2.0.0

NEW FEATURES

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

DOCUMENTATION

• Added a new vignette focused on gene-set analysis

piano 1.22.0

DOCUMENTATION

• Update installation instructions in the vignette

piano 1.20.1

DOCUMENTATION

• Updates to GitHub landing page (README.md)

piano 1.18.1

BUG FIXES

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

piano 1.18.0

DOCUMENTATION

• Switched to accommodate documentation in r-files using roxygen

BUG FIXES

• Fix print addInfo for GSC bug

piano 1.16.4

BUG FIXES

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

piano 1.16.3

BUG FIXES

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

piano 1.16.2

BUG FIXES

• 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.

piano 1.16.1

BUG FIXES

• Fix biomaRt Rchunk in vignette to avoid build error

piano 1.14.5

BUG FIXES

• Reset plot layout after networkPlot.
• 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.

piano 1.14.3

BUG FIXES

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

piano 1.14

NEW FEATURES

• Added new GSA method fgsea (fast GSEA) from the fgsea package.
• Added max method as an option in consensusScores().

IMPROVEMENTS [credits to Alexey Sergushichev

• 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.
• Improved speed of checkLoadArg().
• Improved speed of gene-set statistic calculation for GSEA in calcGeneSetStat().
• Improved speed of FDR calculation for GSEA in fdrGSEA().

BUG FIXES

• Updated NAMESPACE to load dependencies in a better way.
• Updated the parsing of sbml files in loadGSC().
• Updated networkPlot() to conform to changes in the igraph package.

piano 1.12

• No changes

piano 1.10.2

DOCUMENTATION

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

piano 1.10.1

BUG FIXES

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

piano 1.8.2

BUG FIXES

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

piano 1.6.2

BUG FIXES

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

piano 1.6.1

DOCUMENTATION

• Updated this NEWS file

piano 1.6.0

NEW FEATURES

• 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.

piano 1.4.2

BUG FIXES

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

piano 1.4.1

BUG FIXES

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

piano 1.4.0

NEW FEATURES

• Added argument plot to consensusHeatmap() so that drawing the heatmap can be suppressed but the corresponding numerical matrix can be saved.
• 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.
• Added a matrix nGenesMat to the output of consensusHeatmap() containing the same information as printed in the heatmap if argument cellnote="nGenes".
• 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.
• Introduced the new function GSAheatmap(), which is similar to consensusHeatmap() but for only a single gene set result (gsaRes object).

BUG FIXES

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

DOCUMENTATION

• Updated consensusHeatmap() man page according to new changes in the function.
• Added man page for GSAheatmap().

piano 1.2.12

DOCUMENTATION

• Updated the biocViews field in the DESCRIPTION file.

piano 1.2.11

BUG FIXES

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

piano 1.2.10

BUG FIXES

• 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.

piano 1.2.9

BUG FIXES

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

piano 1.2.8

BUG FIXES

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

piano 1.2.7

BUG FIXES

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

piano 1.2.6

BUG FIXES

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

piano 1.2.5

BUG FIXES

• 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.

piano 1.2.4

BUG FIXES

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

piano 1.2.3

BUG FIXES

• Improved error checking of supplied annotation in loadMAdata().
• Improved error checking of chromosome mapping in polarPlot().
• Fixed typo in loadMAdata man page.

piano 1.2.2

DOCUMENTATION

• Updated installation instructions in the vignette.
• Fixed typo in consensusHeatmap man page.

piano 1.2.1

BUG FIXES

• 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.

piano 1.2.0

NEW FEATURES

• Added argument ncpus to runGSA(). Enables parts of this function to run in parallel, thus decreasing runtime. Requires R package snowfall.
• Added function runGSAhyper() to perform gene set analysis using Fisher's exact test, as an alternative to runGSA.
• Added information about genes in each area of the Venn diagram in the output of diffExp().
• Added volcano plot as optional output of diffExp() and added argument volcanoFC.
• 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.
• Added the yeast metabolic model iTO977 to be loaded with loadGSC(), for detecting reporter metabolites using gene set analysis. (See vignette.)
• Added support for running networkPlot() on objects returned by runGSAhyper().

DOCUMENTATION

• Minor updates to the vignette.
• Updated diffExp() man page.
• Restructered this NEWS file.

BUG FIXES

• Updated diffExp() to handle changes in lmFit() and topTable() from limma.
• 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.
• Updated the main legend of the plot from consensusScores() to make it clearer.
• Updated error-messages in networkPlot().
• Fixed typo in PC variance plot produced by runQC().

piano 1.0.7

DOCUMENTATION

• Updated consensusScores() man page.

piano 1.0.6

DOCUMENTATION

• Updated loadMAdata() man page.

piano 1.0.5

BUG FIXES

• 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

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

piano 1.0.4

BUG FIXES

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

piano 1.0.3

DOCUMENTATION

• Updated references in vignette.

piano 1.0.2

DOCUMENTATION

• Updated CITATION information.

piano 1.0.1

DOCUMENTATION

• Updated CITATION information.
• Fixed typos in DESCRIPTION and piano-package.Rd.
• Updated the man file for loadGSC().
• Added URL in DESCRIPTION.

BUG FIXES

• Fixed bug in loadGSC() so that gmt-files are now loaded correctly.
• Temporarily added suppressWarnings() in polarPlot() around the calls to radial.plot() since warnings appeared for example("radial.plot") in plotrix v3.4-6.

piano 1.0.0

NEW FEATURES

• Now part of Bioconductor.
• Removed the arguments 'venn', 'heatmap' and 'polarPlot' from diffExp and replaced them with a new argument: 'plot'.
• The consensusScores function now does not return its result invisibly.
• The argument order in consensusScores has changed: 'plot' has been moved from last place to after 'method'.
• Removed contrastName as output from runGSA and geneSetSummary, including man pages.
• Changed name of folder for example data from exampleData to extdata, and updated man pages and vignette.
• Changed so that total number of gene-level statistics are printed during run, instead of total number of unique genes.

DOCUMENTATION

• Added citation DOI to vignette.
• Updated the man page for consensusScores, added correct output description.
• Updated the Description field text in the DESCRIPTION file.
• Changed the man page for consensusHeatmap clarifying that the cutoff argument is consensus score (not rank)
• Updated the man page for loadGSC, clarifying the input.
• Reworked the vignette to fit Bioconductor, removed section on R introduction.
• Removed 'typical usages' section from man page of loadMAdata since this is covered in the vignette.
• Updated the examples for diffExp, networkPlot, consensusHeatmap and consensusScores to show how to handle the returned object.
• Added CITATION file.
• Added NEWS file.
• Added more links to similar packages in runGSA help page.
• Updated the installation instructions in the Vignette to fit Bioconductor.

BUG FIXES

• Fixed bug in geneSetSummary when no directions are available.
• Fixed a bug in diffExp() regarding the result table, when gene names (annotation) are not available
• Fixed a bug in diffExp() so that the heatmap shows gene names if available, otherwise the probeset IDs
• Removed man page for internal functions.
• Updated the loadMAdata function to use the justPlier function from package plier, instead of a modified version.
• Removed internal function justPlierSpec.