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Changelog
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Note: as of 2009/03/10, changes that lead to different calculational results are marked as DIFF.
2018/10/22: 1.66
. Function consensusDissTOMandTree is now a it faster because of more
efficient garbage collection.
. Function verboseBarplot can now optionally add text labels to the
(also optional) scatterplot.
. In internal functions plotting heatmap legends, widths are now
specified in inches rather than in user coordinates.
. Hierarchical consensus module merging is now more robust to unusual
cases with 0 or only 1 module.
. Bugfix in hierarchicalConsensusModules: supplying a single
networkOptions dows not produce an error.
. pruneAndMergeConsensusModules now checks for presence of at least
one module; if no modules are present, it returns the input labels
rather than throwing an error.
. DIFF: Bugfix in hierarchicalConsensusModules changes the order of
imputation and removal of genes and samples with too many missing
values. This may lead to slightly different module eigengenes.
2018/10/02: 1.65
. Bugfix in modulePreservation fixes duplicate rownames error.
. Function signedKME now checks that colnames of the input data are
unique and makes them unique if not.
. Consensus calculations now return origin count for all consensus
quantiles and the mean consensus. Origin count for each set is the
number of (calibrated) values from the set that are less than or equal
the consensus.
. New function consensusTreeInputs for getting inputs of a consensus
tree.
2018/09/24: 1.64-81
. Fixed crash in softConnectivity when weights are used.
. Fixed bug in labeledHeatmap that transposed a 1-row matrix into a
1-column one.
. Fixed minor typos in errors emitted by labeledHeatmap.
2018/09/14: 1.64-80
. empiricalBayesLM now accepts optional argument fitToSamples that can
restrict the fitting process to a subset of samples. The argument
order was also rearranged to make the order more logical.
2018/09/09: 1.64-1
. binarizeCategoricalColumns.for... have re-ordered and in some cases
added arguments to make them more useful.
2018/09/05: 1.64
. Web site link updated
. Documentation for cor has been improved by making more precise what
nThreads actually affects
. Documentation for pickSoftThreshold.fromSimilarity has been improved
thanks to a suggestion from Paolo Inglese.
. Function signedKME has been streamlined and a bug in which gene
names in the output were passed through check.names in coercing the
input to a data frmae is now fixed.
. New functions binarizeCategoricalVariable,
binarizeCategoricalColumns, and related wrappers for binarizing
categorical covariates into sets of binary indicators
. labeledHeatmap now accepts arguments showRows and showCols that
allow one show a subset of the heatmap without having to explicitly
subset all row- and column-specific arguments
. branchSplitFromStabilityLabels.individualFraction can now work with
missing entries in cluster labels
. New function signifNumeric for rounding numeric columns of a data
frame.
. Bugfix in corFast: argument 'use' is now interpreted properly
(thanks to Thomas Mohr for the report).
. Argument networkType has been removed from the function
pickSoftThreshold.fromSimilarity where it has not been used; help
file has been adjusted accordingly (thanks to Max Moldovan for
reporting the issue).
. mtd.mapply now prints a more informative error message.
. bugfix in GOenrichmentAnalysis which now works again.
2018/03/21: 1.63-2
. TOM calculation now gives 0 for completely unconnected nodes,
instead of returning NaN
2018/02/26: 1.63
. Bugfix in blockwiseModules fixes a crash caused by supplying weights
to bicor
. DIFF: correlation options such as maxPOutliers are now by default
used throughout function blockwiseModules. New argument
useCorOptionsThroughout can be used to switch to old behaviour where
the arguments were used only for network construction.
2018/02/10: 1.62
. New functions sampledBlockwiseModules and
sampledHierarchicalConsensusModules carry out network analysis
repeatedly on resampled data.
. TOM calculations can optionally use internal matrix algebra rather
than R- (or system-)provided BLAS, controlled by argument
useInternalMatrixAlgebra.
. Pearson correlation (function cor) now accepts individual sample
weights for arguments x and y. When both weights are supplied (and
for correlation of a columns in a single matrix), the weights are a
product of the weights for the two vectors being correlated.
Denominators are calculated separately using separate weights, which
leads to slightly different results than standard weighted
correlation.
. Most network construction functions now also accept optional weights.
. hierarchicalConsensusModules can now optionally perform gene/module
pruning and merging iteratively.
. New functions pruneConsensusModules and
pruneAndMergeConsensusModules implement the pruning and iterative
pruning/merging of hierarchical consensus modules.
. Network construction functions now accept argument
suppressTOMForZeroAdjacencies whose effect is to set TOM to zero for
all node pairs with zero adjacency.
. Bugfix in individualTOMs: function now works with default
useDiskCache
. Module eigengenes returned by blockwiseConsensusModules now carry
names copied from names of multiExpr
. New function imputeByModule
. Bugfix in verboseBoxplot and verboseBarplot: the function now
honors the setting of addScatterplot and correctly interprets point
color and other arguments when they are vectors.
. Enhancements and bugfixes in TOMplot which should work with all
data sizes and dendrogram complexities.
. Function formatLabels now avoids over-splitting labels that already
contain a newline character.
. Function labeledHeatmap can plot row labels on the right, specified
via argument yLabPosition.
. Bugfix in internal function .networkCalculation
2017/08/04: 1.61
. Bugfix in consensusCalculation: function works with mean consensus.
. New arguments pch and plotPriority for verboseScatterplot.
. Function pmin has been removed since it incorrectly duplicates
base::pmin.
. Function GOenrichmentAnalysis is deprecated. Please use function
enrichmentAnalysis from R package anRichment, available from
https://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/GeneAnnotation/
2017/07/07: 1.60
. empiricalBayesLM expanded with additional arguments allowing
specification of initial fit function
. DIFF: New branch split function that works with stability labels,
branchSplitFromStabilityLabels.individualFraction, that tweaks the
branch dissimilarity measure to work better when one branch is large
and one small. To reproduce old results, use argument
stabilityCriterion = "Common fraction" to functions
hierarchicalConsensusModules and blockwiseConsensusModules.
. verboseBoxplot and verboseBarplot can now optionally overlay
scatterplots of the underlying data (thanks to Zhijin (Jean) Wu for
suggestion and code).
. Bugfix in enrichmentAnalysis: function does work when the number of
reported terms is zero. (Thanks to Zhijie Cao for bug report and
fix.)
. New functionality that allows a hierarchical calculation of
consensus modules, with multiple new functions.
. New arguments colorHeightBase, colorHeightMax control layout in
function plotDendroAndColors
. Arguments controlling the legend size in heatmaps with legends
been tweaked to make the legend width independent of the width of
the plotting region.
. The horizontal adjusting of row labels in labeledHeatmap can now be
set using the new argument x.adj.lab.y.
. Bugfix in mtd.susbet: function now works properly when invert is
TRUE.
. formatLabels can now format strings to a maximum width in user
coordinates and shorten the results to a given number of lines.
. Limitation to block sizes less than the integer addressing limit
(sqrt(2^31)) has been removed.
. Multiple mtd.... functions now return NULL when the input multiData
argument has length zero.
. Function adjacency now accepts corOptions in both character and list
formats.
. New function minWhichMin that calculates the row- or column-wise
minimum and index of the minimum.
. New functions pmin.fromList, pmean.fromList, pquantile.fromList, for
parallel minimum, mean and quantile whose input is a list of
identically sized arrays; functions pmin, pmean and pquantile now
use compiled code and should be substantially faster and more memory
efficient.
. Bugfix in function blockwiseModules: corrected conditional module
removal if too few genes remain.
. pickSoftThreshold is now faster thanks to Alexey Sergushichev; new
argument gcInterval allows the user to fine tune frequency of garbage
collection to suit the size of the data.
. verboseBarplot now takes argument ylim which defaults to
incorporating all bar heights plus error bars (if requested)
. Cleanup in function labeledHeatmap: incorrect text and color label
offsets and widths fixed. The corresponding arguments xColorWidth,
yColorWidth are now measured in user units rather than fractions of
overall width and height.
. New functions bicovWeightFactors and bicovWeightsFromFactors
2016/05/30: 1.52
. New function plotMultiHist for plotting multiple histograms in one
plot
. New functions multiGrep, multiGrepl, multiSub, multiGSub
. New argument invert in mtd.subset allows consistent excluding of
rows and columns from multiData structures.
. Bugfix in modulePreservation: accuracy statistics now work also with
a single module. Thanks to Victor Hanson-Smith for pointing this
out.
. mtd.rbindSelf now warns when colnames of the individual data sets do
not agree.
2016/03/08: 1.51
. DIFF: Defaults for the number of pre-clustering centers in
blockwise[Consensus]Modules, projectiveKMeans and
consensusProjectiveKMeans have changed to prevent the
pre-clustering from becoming too long. To reproduce old results, use
(nPreclusteringCenters or nCenters) = min(nGenes/20,
maxBlockSize^2/nGenes), where nGenes is the number of genes (variables)
in the input data.
2016/02/23: 1.50
. Bugfix in function cor: function now correctly handles cases where
columns have missing data placed such that the remaining entries
(after removing missing values) have zero variance. Thanks to Pasha
Mazin for pointing this out.
. New function consensusRepresentatives for selecting consensus representatives
from multi-data.
. Cleanup in plotOrderedColors should results in better placement of
'rowText' under blocks of colors.
. Minor change in spacing for row text in plotOrderedColors that also affects
plotColorUnderTree and plotDendroAndColors
. TOM calculation functins (TOMsimilarity, blockwiseIndividualTOMs,
blockwiseModules) now accept argument replaceMissingAdjacencies that
allows the underlying code to replace missing adjacencies with an
appropriate value for zero-strength link.
. moduleEigengenes is now more resistant to problems with missing data
and zero-variance variables.
2015/12/27: 1.49
. DIFF: goodGenes, goodGenesMS, goodSamplesGenes, goodSamplesGenesMS get an
argument `tol' to compare the variance against, rather than against
zero. This prevents erroneous retaining of zero-variacen genes
because of numeric under/overflow errors in the fast calculation of
variance. This may possibly result in removal of genes that were
retained in WGCNA versions 1.47-2 and newer, but should remove the
same genes as 1.47-1 and older.
2015/12/16: 1.48-2
. Bugfix in our local copy of heatmap, called from TOMplot, based on
the bug report
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16583 . Thanks to
Duncan Murdoch for pointing it out
. Function goodSamplesGenesMS can now work with data frames within the
multiExpr structure, rather than just matrices.
2015/11/03: 1.48-1
. TOMplot now uses my own dendrogram drawing routine which should not
run into the stack/memory allocation problems of the standard
plot.dendrogram function.
2015/10/29: 1.48
. Bugfix in pickHardThreshold (and pickHardThreshold.fromSimilarity):
when the input is a similarity matrix rather than expression data,
the function no longer crashes.
2015/10/09: 1.47-6
. Bug in consensusTOM fixed that caused a spurious error
"File names to save blocks of consensus TOM are not unique."
when calculating with more than on block.
. DIFF: Function consensusProjectiveKMeans can (and will by default) impute
missing data. This may cause differences in preclustering when
missing data are present. To reproduce old results, use
argument imputeMissing = FALSE.
2015/09/30: 1.47-5
. Function consensusKME is now using internal code for re-arranging
rather than relying on reshape's melt-cast combination due to
performance issues with larger data sets.
. Imports from/dependence on reshape have been dropped.
. blockwiseConsensusModules accepts argument cacheBase which replaces
the default "." that has been used.
. labelPoints now returns a data frame with the label positions, and
accepts argument doPlot that optionally turns off the plotting of
the labels.
. bicor now produces a better-worded warnings about zero or missing
MAD.
2015/08/07: 1.47-4
. DIFF: projectiveKMeans now by default imputes missing data in
datExpr at the start of the function.
This can lead to somewhat different output; old
behaviour can be forced by setting imputeMissing = FALSE. This
change does not affect blockwiseModules since blockwiseModules
imputed missing data before calling projectiveKMeans.
. Internal code cleanup: several ifelse calls changed to if else
constructs to avoid issues with ifelse generics defined by
bioconductor
. pickHardThreshold is now more resistant to genes (columns) that have
zero variance. However, their connectivity is considered 0.
. DIFF: Bugfix in internal code fixes an error in blockwiseModules and
blockwiseConsensusModules where blocks determined by pre-clustering
were incorrectly merged. In rare cases this may cause differences to previous
results. Thanks to Elmar Tobi for reporting this.
2015/06/27: 1.47-2
. goodGenes and goodSamples, along with their MS versions, should now
run faster thanks to a code clean-up
2015/06/18: 1.47-1
. Bugfix in empiricalBayesLM fixes a crash in the function.
2015/06/13: 1.47
. Functions plotCor, plotMat and rgcolors.func from sma have been re-introduced
. empiricalBayesLM is now more robust to missing values, particularly
when OLS regression fails due to missing values making some of the
covariates constant.
. Bugfix in bicovWeights fixes crash when there is one variable with
MAD = 0.
. Function blockwiseModules can now optionally use module merging
criteria derived from stability studies.
. Functions blockwiseModules, blockwiseIndividualTOMs and
consensusBlockwiseModules now accept argument blockSizePenaltyPower
that lets the user specify the severity of penalty for blocks
exceeding maximum size.
. Functions projectiveKMeans and consensusProjectiveKMeans now accept
Inf for sizePenaltyPower.
. Function labeledHeatmap.multiPage now accepts more explicit
arguments (rather than relying on ... as before)
and correctly handles separator lines.
2015/03/28: 1.46
. Functions inherited from the now-defunct package sma have been
removed.
2015/03/27: 1.45
. New function empiricalBayesLM for removing unwanted variation due to
given covariates from high-dimensional data
. New function bicovWeights for assigning weights to observations
based on whether they are suspected outliers
. labeledHeatmap and friends now accept argument keepLegendSpace
. labeledHeatmap now returns information about positions of individual
boxes in the heatmap.
. labeledHeatmap now accepts argumens xColorOffset and yColorOffset
controling the gap between color labels and the heatmap itself.
2015/02/06: 1.43-11
. Bugfix in C code fixes memory allocation errors with large data
sets. The C code was also made more consistent in the use of
size_t whenever needed and possible.
. Bugfix in labeledHeatmap fixes the direction of extended separator
lines for x-axis labels with angle other than the default 45
degrees.
2015/01/23: 1.43-10
. Bugfix in function blockwiseIndividualTOMs and functions that use it
(blockwiseConsensusModules, consensusTOM) fixes a bug that caused
crashes when more than one blocks were used.
2015/01/15: 1.43
. Package now imports AnnotationDbi and GO.db
. Function blueWhiteRed gains argument endSaturation that allows the
user to lighten the colors at the end of the range, at the expense of
saturation.
. Function labeledHeatmap gains additional arguments allowing the user
to place horizontal and vertical divider lines into the heatmap.
. Bugs introduced into GOenrichmentAnalysis in the previous release
are now fixed.
2014/11/25: 1.42
. Function TrueTrait has been re-worked and the argument Strata to it
is no longer accepted.
. labeledHeatmap.multiPage now works with 1-column or 1-row matrices.
. The textMatrix argument to labeledHeatmap and
labeledHeatmap.multiPage is now allowed to be a (dimensionless)
vector as long as its length is consistent with the dimensions of
the input Matrix.
. Bugfix in function formatLabels fixes sometimes incorrect start of
formatted labels.
. Bugfixes in function TrueTrait
. DIFF: Bugfix in mtd.branchEigengeneDissim that primarilly affects
blockwiseConsensusModules. The consensus quantile was incorrectly
applied, which led to overly aggressive module merging. The bugfix
will lead to a different final modules if useBranchEigengeneDissim
was TRUE. To reproduce old behavior, use argument
reproduceBranchEigennodeQuantileError = TRUE.
. New function consensusTOM implements calculation of consensus TOM
in a stand-alone function; this calculation was previously hidden
inside blockwiseConsensusModules.
. Network calibration methods in consensusTOM now include full
quantile normalization
. DIFF: bugfix in blockwiseIndividualTOMs that affects
blockwiseIndividualTOMs as well as blockwiseConsensusModules: The
soft-thresholding power for set 1 was used for all sets. This bug
has bow been fixed; to reproduce old calculations, change the old
code to use the same power for all sets. I apologize for this rather
serious omission.
. blockwiseIndividualTOMs gains additional output components.
. Internal C code changed some index variables from int to size_t.
. Function individualTOMs now uses a more memory-efficient way to call
the internal compiled code.
. Bugfix in mtd.apply fixes occasional spurious crashes
. Function mtd.apply now copies the 'names' attribute from input to
the output
. Function mtd.subset can now subset columns based on column names,
not just numeric indices.
. Function votingLinearPredictor can now tolerate missing data in the
predictor variables (features).
. blockwiseModules gains a new argument loadTOM.
2014/06/13: 1.41-1
. DUP = FALSE removed from all .C calls since the argument is
deprecated. This means that memory requirements may increase in some
situations.
2014/06/12: 1.41
. New function shortenStrings
. Changed several packages we depend on from Depends: to Imports:
. New functions prependZeros and formatLabels
. Bugfix in userListEnrichment: function no longer crashes when there
are no "significant" overlaps
. New function intramodularConnectivity.fromExpr
2014/05/07: 1.40
. Functions blockwise[Consensus]Modules and
recut[Blockwise,Consensus]Trees get new arguments minSplitHeight and
minAbsSplitHeight that get passed to cutreeDynamic.
. Arguments for blockwiseModules have been re-ordered to group them
and make it easier to find the right setting.
2014/04/28: 1.39
. Function exportNetworkToVisANT can now restrict connections to a
given number of top connections.
. Function exportNetworkToVisANT returns the resulting data frame
invisibly.
. Function modulePreservation gains the ability to run the
calculations in parallel, controlled by argument
'parallelCalculation'.
. Function modulePreservation gains the ability to explicitly specify
test sets for each reference network, via parameter testNetworks.
. Functions matchLabels and overlapTable have been expanded with new
functionality and arguments. matchLabels now works with any labels
(not just numeric or color labels) and can handle missing labels by
removing them.
. Bug in function multiData2list fixed: function now returns a simpler
(and correct) list.
. Crash-causing bug in mtd.rbindSelf fixed.
2014/01/08: 1.37
. New functions multiUnion and multiIntersect
. New function labeledHeatmap.multiPage produces labeled heatmaps
divided into multiple plots (pages).
. plotColorUnderTree and plotOrderedColorsnow produce more precise
"center" and "right" text alignment.
. Maximum block size in blockwiseModules, blockwiseConsensusModules
and blockwiseIndividualTOMs (argument 'maxBlockSize') is now limited
to be less than sqrt(2^31) to prevent problems with C and Fortran
routines. The same limitation also applies to the 'preferredSize'
argument of projectiveKMeans and consensusProjectiveKMeans.
. Occasional bug when saving and loading permutation test results in
modulePreservation fixed.
2013/11/22: 1.36
. Needs dynamicTreeCut 1.61 or higher.
. Bugfix in mtd.mapply fixes a crash.
. Warning message in mtd.subset cleaned up.
. New function multiData to conveniently create multiData structures.
. The color palette of blueWhiteRed has been tweaked to provide
lighter extreme colors which makes it easier to read black text
superimposed on the strongest colors.
. More descriptive error message in cor() and bicor() when input
contains missing data and 'use = "all.observations"'.
2013/11/04: 1.35
. Function accuracyMeasures now works also with factors.
. Function moduleEigengenes calls impute.knn only if there are any
missing data.
. Functions mtd.apply, mtd.applyToSubset, and mtd.mapply gain
arguments controling whether and how progress should be displayed;
they also gain arguments that let the user specify calculation on
only a subset of the input sets.
2013/10/10: 1.34
. Function verboseBarplot gains argument addCellCounts that enables
display of counts above each bar.
. Function mtd.subset gains the argument 'permissive' that allows
subsetting of "loose" multiData structures as well as 'drop' that
controls dropping of dimensions with extent 1.
. Internal: Depends and Imports fields were cleaned up as per new CRAN
requirements. Users should be aware that loading and attaching WGCNA
now does not automatically attach all packages from which WGCNA imports.
. Potentially serious bug has been fixed in the internal C code for
calculations of correlation (function cor()). This bug seems to have led to
correlation sometimes returning 0 where it should have returned an NA.
2013/08/29: 1.33
. mtd.apply and mda.applyToSubset gain argument mdaCopyNonData that controls whether
non-data components of input should be copied to output
. Bug in matchLabels fixed that led to non-integer color labels if two
reference modules had the same size.
. New function plotOrderedColors that extends plotColorUnderTree to
the case where the plot 'above' is not a dendrogram but a general plot
(a useful example is a barplot).
. DIFF: bugfix in blockwiseModules, recutBlockwiseTrees,
blockwiseConsensusModules, recutConsensusTrees: gene reassignment by
kME now reassigns correct genes. Previously, the the reassigned
genes were incorrectly chosen. This may make a small difference in
the module assignments if reassignThreshold was above zero (as it
was by default). The default was also changed to not perform module
re-assignment.
. Switching to dynamicTreeCut 1.60: this dynamicTreeCut uses external
criteria that are supplied by the blockwise* functions. The
criteria are implemented in functions branchEigengeneDissim,
mtd.branchEigengeneDissim, branchSplit, branchSplit.dissim
To preserve results of older calculations, new features are disabled
by default.
. New functions for convenient handling of multiData structures:
mtd.apply, mtd.applyToSubset, mtd.mapply, mtd.rbindSelf,
mtd.setAttr, mtd.colnames, mtd.setColnames mtd.simplify
mtd.subset, list2multiData, multiData2list, isMultiData
. Function randomGLMPredictor has been removed. Please use the package
randomGLM and the function randomGLM in that package.
. Internal C code has been simplified.
2013/07/20: 1.30
. Functions blockwiseModules and TOMsimilarityFromExpr are now more
memory-efficient: only 2 copies of the potentially large TOM matrix
are needed, down from 3 before.
. Function mergeCloseModules can now optionally perform quantile
equalization (normalization) on to make eigengene (dis-)similarities
comparable across the data sets.
. Argument order in mergeCloseModules has changed to a more logical
order
2013/07/18: 1.29
. Functions determining the number of available cores are now more
robust.
. labeledHeatmap gains argument naColor that controls the color for
missing values.
2013/07/09: 1.28
. Help files formatted to narrower line width.
. bugfix in pickSoftThreshold when dataIsExpr is FALSE: function now
correctly checks similarity (thanks to Lourdes Pena Castillo for
reporting it).
. updateProgInd now only updates display if the value to be displayed
is actually different from the one already displayed. This can lead
to somewhat better performance if updateProgInd is the performance
bottleneck.
. DIFF: Bug fix in GOenrichmentAnalysis: all evidence codes listed on
http://www.geneontology.org/GO.evidence.shtml are now recognized.
This will likely may change GO enrichment results. We apologize for
this omission.
. Bug fix in userListEnrichment: p-values of comparisons with no
overlapping genes are now 1, instead of 0.
. plotColorUnderTree and plotDendroAndColors gain new arguments
rowTextAlignment and rowTextIgnore that afford more flexibility in
how the row text is formatted.
2013/04/01: 1.27-1 ("This one's no April 1 joke!")
. userListEnrichment now contains a new set of gene lists compiled mostly by Mike
Palazzolo and Jim Wang at CHDI.
. userListEnrichment now runs faster
. Bug fix in verboseBarplot: p-values are now consistently diplayed
with two significant digits.
. Bug fix in blockwiseConsensusModules: function now works correctly
(and faster) when not using disk cache
2013/03/06: 1.26 ("Spring growth")
. Bug fix in blockwiseModules, blockwiseConsensusModules and
blockwiseIndividualTOMs: functions now use consisten block labels
[thanks to Austin Hilliard for pointing it out].
. Function accuracyMeasures has been re-written to accept directly
vectors of predicted and observed values, and work also for
prediction of continuous outcomes. The new function is
backwards-compatible with older versions except for the name of the
first argument.
. Function verboseScatterplot gains a new argument displayAsZero that
allows displaying small correlations as 0 (rather than say 1e-13).
. New function returnGeneSetsAsList returns gene sets used by function
userListEnrichment.
2012/12/01: 1.25-2 ("We ain't done fixin' yet")
. Bugfix in blockwise[Consensus]Modules fixes a crash under certain
circumstances (when some of the initial modules are removed).
[Thanks to Nicola Soranzo for pointing this out.]
. Bad choice of return value in WGCNAnThreads() that caused a crash in
pickSoftThreshold is now fixed. [Thanks to multiple users who
noticed this.]
2012/11/09: 1.25-1 ("The Election Fix")
. Internal C++ code now compliant with older compilers that don't
implement vector::data()
2012/11/06: 1.25 ("The Election Issue", pardon the pun.)
. DIFF: bugfix in function modulePreservation: the function now
respects the corFnc and corOptions arguments throughout the
calculations. This bug affected calculations that used correlation
functions other than the default "cor" and options other than
the default "use = 'p'".
. Introducing parallelization to user-level R functions through the use
of packages parallel, foreach and the doParallel backend. The parallelization
should work on all R-supported platforms. This change does not
affect C-level workhorse functions for calculating correlations.
. New function blockSize that attempts to choose a suitable block size
for most functions that use a block-wise approach to fit
calculations into memory.
. Function labels2colors is now more robust and should work for
data.frames as well
. Function verboseBoxplot gains arguments notch and varwidth that are
passed to the underlying boxplot call.
. Functions plotDendroUnderTree and plotDendroAndColors now
display missing color values as grey.
. Function verboseBarplot can now handle binary variables as well and
will print Fisher exact test p-value.
. Function colQuantileC now ignores missing data
. Internal C code cleaned up and small memory leaks plugged.
. Function labelPoints has a new argument protectEdges that can
prevent labels from going outside of the plot area.
. verboseScatterplot now has explicit arguments col and bg to specify
colors and fill (background) of the plotting symbols. This makes
specifying col and bg work also when only a sample of all points is
plotted.
. GOenrichmentAnalysis can now optionally shorten output by omitting
details of highest-enriched GO terms.
. Defaults in randomGLMpredictor have been slightly tweaked for better
performance.
. New function transposeBigData for transposing big matrices.
2012/08/02: 1.23-1
. Examples in help files are now shorter to speed up execution as per
CRAN requests.
2012/07/27: 1.23
. Function userListEnrichment is now improved with more categories of
gene lists
. DIFF: bugfix in functions corAndPvalue and bicorAndPvalue:
calculation of the Z statistic is now corrected. This bug did not
affect the calculetion of Student t statistics nor the p-values.
. Function standardScreeningBinaryTrait gains argument areaUnderROC
(default TRUE) that allows the user to turn off AUC calculation and
thus achieve a substantial speedup for large data sets.
. Function metaAnalysis now by default turns off AUC calculation,
making it much faster on large data sets. The AUC calculation can be
enabled using the new argument getAreaUnderROC.
. New function randomGLMpredictor that implements an ensemble predictor based on
bootstrap aggregation (bagging) of generalized linear models whose covariates
are selected using forward stepwise regression according to AIC criteria.
2012/06/18: 1.22
. DIFF: Bugfix in function blockwiseConsensusModules: the module colors are
now correct (and not scrambled) when some genes are excluded due to
too many missing entries. Apologies for any non-sense results this
error may have generated.
. Bugfix in the function modulePreservation when used on adjacency
input: clustering coefficient calculations are now corrected.
. Function modulePreservation gains an additional argument
calculateClusterCoeff, with default value FALSE, that can be used to
enable/disable clustering coefficient calculations. These tend to be
slow and for efficiency purposes the default is FALSE.
. DIFF: because of the above, clustering coefficient calculations in
function modulePreservation are disabled as a default.
. Error message in modulePreservation about input containing genes
with too many missing values is now more informative.
. Bugfix in function numbers2colors: function now properly accounts
for the presence of positive and negative entries when automatically
deciding whether the input should be considered signed or unsigned.
. Function rankPvalue now doesn't warn about weights not summing to 1.
. DIFF: bugfix in function userListEnrichment corrects output.
Previously, UNcorrected p-values were returned when corrected
p-values were requested, and no p-values were returned when
uncorrected p-values were requested.
. p-value display in function verboseBarplot is now cleaned up by
properly arranging spaces.
. Bugfix in mergeCloseModules: function now completes correctly when
all modules are merged into a single module.
. Internal bugfix in C function minWhichMin: function now works
correctly when the first entry is NA or NaN.
2012/04/23: 1.20
. New function blueWhiteRed that produces a color sequence
distinguishable by people with the most common kind of color
blindness (green-red color blindness). The currently much-used
greenWhiteRed now outputs a warning to that effect. We recommend
that users switch to blueWhiteRed.
. The default color palette for numbers2colors is now blueWhiteRed.
. Function TOMsimilarity now forces the diagonal of the input
adjacency matrix to be 1. The diagonal is not really meaningful in a
network analysis, but the underlying C code assumes the diagonal to
be 1 since it simplifies calculations. This change also applies to
TOMdist (which calls TOMsimilarity).
. Function blockwiseConsensusModules now accepts argument
trimmingConsensusQuantile and makes the consensus in module trimmimg
consistent with the consensus in network construction and
module identification.
. Function recutConsensusTrees now accepts arguments trimmingConsensusQuantile
and mergeConsensusQuantile with the same effect as in
blockwiseConsensusModules.
. Removed argument minKMEtoJoin from blockwise* and recut* functions as it has
not been used by the actual code.
. Function verboseBarplot now accepts argument horiz and is capable of
creating horizontal barplots.
. Internal: C function minWhichMin now ignores missing values.
2012/02/28: 1.19
. Argument name change in function TOMplot: colors and colorsLeft are
now Colors and ColorsLeft to avoid conflict with argument col to
functions heatmap and image.
. Bugfix in internal function .consensusMEDissimilarity that caused crashes
mergeCloseModules.
. DIFF: blockwiseConsensusModules now passes the argument mergeConsensusQuantile
to mergeCloseModules, which can lead to different module merging
compared to previous versions. Use mergeConsensusQuantile = 0 to
reproduce results from older versions of this package.
. Function mergeCloseModules now takes arguments consensusQuantile,
corFnc and corOptions
. New function blockwiseIndividualTOMs to calculate individual TOMs
across multi-set expression data
. New functionality in blockwiseConsensusModules that can now utilize
pre-calculated individual TOMs, giving more flexibility
. New utility function lowerTri2matrix
. Internal change: default chunk size in consensus module calculation
is now 1e8 instead of 1e7. Most computers with at least 2GB of
memory should be able to handle as much; the size can be lowered (or
increased) if necessary.
. Function sizeGrWindow now calls dev.new rather than X11
. New function nSets to directly return the number of sets in a
multi-set variable.
. Function verboseBarplot now returns the midpoints of the drawn bars
(as the function barplot does) augmented by the bar heights as
attribute "height".
. Minor changes and cleanup in code
. New citation added for our JSS article
2012/01/12: 1.18-2
. Bugfix in function consensusKME fixes column names of output
2012/01/04: 1.18-1
. Bugfix in function GOenrichmentAnalysis fixes occasional crash of
the function
2011/12/22: 1.18
. DIFF: p-value calculation in userListEnrichment is now corrected
to give the probability of overlap **as strong or stronger** than observed,
rather than that of overlap **stronger** than observed. The resulting
p-values are more conservative; the difference can be large for very small
categories.
. metaAnalysis and consensusKME now also calculate meta-analysis
statistics using weights proportional to the square root
of the number of samples
. Added citation information for the package. The citation is available
by typing the command citation("WGCNA"). Please cite the package
if you use it in published research. (The citation("WGCNA") gives