NEWS

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a4Base 1.37.3

• fix specification of link for fct with different name help page

a4Base 1.37.2

• use Imports rather than Depends + use roxygen2 for documentation
• use Authors@R
• replace toptable (deprecated in limma 3.36.0) by limma:::.topTableT

a4Base 1.37.1

• spectralMap: fix legend win-32

a4Base 1.4.1

• plot1gene now coerces the 'groups' variable to a factor in plot1gene

a4Base 1.4.0

• release for BioC 2.10

a4Base 1.2.4

• throw error in case 'group' variable contains missing values in spectalMap

a4Base 1.2.3

• circumvent build issues on certain versions of windows

a4Base 1.2.2

• more appropriate handling of the dots argument in plot1gene

a4Base 1.2.1

• fix in legend for spectralMap

a4Base 1.2.0

• release for BioC 2.9

a4Base 1.1.4

• fix in limmaTwoLevels

a4Base 1.1.3

• update for revised glmnet package

a4Base 1.1.1

• on BioConductor

a4Base 0.0-26

• better argument handling for mpm

a4Base 0.0-25

• fix histPvalue for limma objects
• add histPvalue method for MArrayLM objects

a4Base 0.0-24

• add proper support for the main argument in histPvalue methods.

a4Base 0.0-23

• add support for cex, cex.lab, cex.main to plot1gene

a4Base 0.0-22

• allow for specifying xlab and ylab in histPvalue

a4Base 0.0-21

• move annotationTable tests to the a4Reporting package
• complete documentation for histpvalue plotter
• added heatmap.expressionSet
• fix legend for spectralMap

a4Base 0.0-20

• topTable method for limma objects gains default setting for n (n=10) and looses default for coef (in order to force people to make the right choice instead of the previous default of 2)
• removed nlcv dependency to speed up loading a4
• remove RColorBrewer dependency (speed up loading)
• changed column names of featureData to be concordant with BioConductor nomenclature
• split off a4Core, a4Preproc and a4Classif packages and become a4Base

a4Base 0.0-19

• move $SRC_PKG/etc to $SRC_PKG/inst/etc as tooltip.script (plotLogRatio) needs to be available at $INSTALLED_PKG/etc

a4Base 0.0-18

• add varEqual argument to tTest (defaults to FALSE)
• improved y axis annotation for volcanoPlot

a4Base 0.0-17

• remove confusionMatrix generic as it is defined already in nlcv; otherwise the one in nlcv is masked

a4Base 0.0-16

• fix colors of groups in spectralMap (now uses a4palette)
• redefine topTable method for MArrayLM objects (is overwritten in nlcv)
• add gene argument (as alternative to probeset) for plot1gene function
• add default pointLabels in case pointLabels for volcanoPlot and its numeric,numeric,missing-method

a4Base 0.0-15

• fix plot1gene (respect order of factor levels in phenoData of ExpressionSet)

a4Base 0.0-14

• bug in volcanoPlot (lods values should be sorted in increasing order, contrary to P values)
• add probe2gene argument to plot1gene
• add topTable method for tTest objects
• set default sub for spectralMap to sub=""
• fix pamClass and corresponding topTable (silence it)
• added xtable for topTable of pamClass
• add nlcvTT data to package
• expose a4palette function to user and document
• add histPvalue for limmaResult object
• turned propDEgenes into generic
• expose volcanoplotter to user and document
• add probe2gene argument to tTest, pamClass, rfClass (defaults to TRUE)
• significant improvements to documentation

a4Base 0.0-13

• fix seemingly inverted logic of topPValues and topLogRatios in volcanoPlot
• reduce space between left 'wing' of volcanoPlot and y axis
• extended volcanoPlot documentation
• integrate annotationTable package into a4
• improve topTable for rfClass and fix xtable method accordingly
• adapt rfClass to improved varSelRF 0.7-1 which now has a verbose=FALSE option that also silences gc() output (patches Tobias Verbeke)
• add documentation for topTable methods
• fix typo print.topTablePam

a4Base 0.0-12

• volcanoPlot made generic, methods for 'limma', 'tTest' and numeric vectors 'x' and 'y'

a4Base 0.0-11

• add varSelRF wrapper rfClass
• add new addGeneInfo function to produce ExpressionSet objects similar to the pipeline
• topTable method (and corresponding print and xtable methods) for lasso models
• topTable method (and corresponding print and xtable methods) for rfClass models
• topTable method (and corresponding print and xtable methods) for pamClass models

a4Base 0.0-10

• add lassoClass
• extract probe2gene function out of spectralMap.R into probe2gene.R
• improve display of sample names in spectralMap

a4Base 0.0-9

• fix pamr error handling mess
• documentation fix in spectralMap
• added mpm.args argument to set arguments for mpm (rationale: allow for PCA)

a4Base 0.0-8

• fixed volcanoPlot (used two devices)

a4Base 0.0-7

• split up again into separate nlcv and a4 packages

a4Base 0.0-6

• updated vignettes

a4Base 0.0-5

• merged nlcv 0.1-72 into the a4 package

a4Base 0.0-4

• added limmaTwoGroups function
• removed dependency on nlcv (to avoid circular dependencies)

a4Base 0.0-3

• insert (basic) vignette on comparison of two groups
• fix new page (grid) for volcanoPlot
• improved y-axis annotation for volcanoPlot
• add probe2gene argument to spectralMap for alternative labeling of points (needs mpm >= 1.0-10)
• added name space to hide probe2gene function
• explicited makeLognormal argument for spectralMap
• changed selection of points to label in volcanoPlot (union of topPvalues and topLogRatios)

a4Base 0.0-2

• spectralMap added

a4Base 0.0-1

• volcanoPlot added