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.