Man pages for a4Base
Automated Affymetrix Array Analysis Base Package

a4paletteUtility function that defines a color palette for use in a4
addQuantilesColorsCompute quantiles for plotGeneDE function
boxPlotCreate a boxplot for a given gene.
combineTwoExpressionSetCombine two ExpressionSet objects
computeLogRatioSummary statistics for gene expression
createExpressionSetcombine gene expression and phenotype data onto a...
ExpressionSetWithComputation-classClass "ExpressionSetWithComputation"
filterVarIntFiltering on Intensity and Variance
heatmap.expressionSetImage plot of an expressionSet
histPvaluePlot the Distribution of P Values
histpvalueplotterWorkhorse function for the histPvalue function
lassoRegMultiple regression using the Lasso algorithm as implemented...
limmaRegWrapper for the limma function for the comparison of two...
limmaTwoLevelsWrapper for the limma function for the comparison of two...
logRegLogistic regression for predicting the probability to belong...
nlcvTTData to Demonstrate nlcv and Co Functions
oaColorsPick One or More OA Colors
oaPaletteGenerate a Palette of OA Colors
plot1geneCreate a Profile Plot for a given Gene
plotComb2SamplesPlots the correlation in gene expression between two samples
plotCombination2genesPlot a Combination of Two Genes
plotCombMultSamplesPlots the correlation in gene expression between more than 2...
plotLogRatioPlot a summary gene expression graph
probabilitiesPlotFunction to plot the probabilities to belong to a certain...
probe2geneTranslate Affymetrix probeset IDs into gene symbols
profilesPlotPlot expression profiles of multiple genes or probesets Plot...
propDEgenesGeneric function to compute the proportion of differentially...
propdegenescalculationEstimation of proportion of differentially expressed genes
propDEgenes-methodsGeneric function to compute the proportion of differentially...
replicatescomputes replicates across a vector
spectralMapGeneric function to draw a spectral map, according to JnJ...
spectralMap-methodsMethods for Function spectralMap according to JnJ Standards
topTable-methodsMethods for topTable
tTestUse t Test to Compare Two Groups
volcanoPlotDraw a Volcano Plot
volcanoPlot-methodsDraw a Volcano Plot
volcanoplotterWorkhorse function for the different volcanoPlot methods
a4Base documentation built on Nov. 8, 2020, 5:41 p.m.