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.