Automated Affymetrix Array Analysis Base Package

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Documentation for package ‘a4Base’ version 1.54.0

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a4palette Utility function that defines a color palette for use in a4
addQuantilesColors Compute quantiles for plotGeneDE function
boxPlot Create a boxplot for a given gene.
combineTwoExpressionSet Combine two ExpressionSet objects
computeLogRatio Summary statistics for gene expression
createExpressionSet combine gene expression and phenotype data onto a ExpressionSet object
ExpressionSetWithComputation-class Class "ExpressionSetWithComputation"
filterVarInt Filtering on Intensity and Variance
heatmap.expressionSet Image plot of an expressionSet
histPvalue Plot the Distribution of P Values
histPvalue-method Plot the Distribution of P Values
histpvalueplotter Workhorse function for the histPvalue function
lassoReg Multiple regression using the Lasso algorithm as implemented in the glmnet package
limmaReg Wrapper for the limma function for the comparison of two groups (two factor levels)
limmaTwoLevels Wrapper for the limma function for the comparison of two groups (two factor levels)
logReg Logistic regression for predicting the probability to belong to a certain class in binary classification problems
nlcvTT Data to Demonstrate nlcv and Co Functions
oaColors Pick One or More OA Colors
oaPalette Generate a Palette of OA Colors
plot1gene Create a Profile Plot for a given Gene
plotComb2Samples Plots the correlation in gene expression between two samples
plotCombination2genes Plot a Combination of Two Genes
plotCombMultSamples Plots the correlation in gene expression between more than 2 samples
plotLogRatio Plot a summary gene expression graph
probabilitiesPlot Function to plot the probabilities to belong to a certain class in binary classification problems.
probe2gene Translate Affymetrix probeset IDs into gene symbols
profilesPlot Plot expression profiles of multiple genes or probesets Plot expression profiles of multiple genes or probesets. Each line depicts a gene, and the color legend can be used to identify the gene.
propDEgenes Generic function to compute the proportion of differentially expressed genes that are present
propDEgenes,limma Generic function to compute the proportion of differentially expressed genes that are present
propDEgenes,numeric Generic function to compute the proportion of differentially expressed genes that are present
propDEgenes-method Generic function to compute the proportion of differentially expressed genes that are present
propDEgenes-methods Generic function to compute the proportion of differentially expressed genes that are present
propdegenescalculation Estimation of proportion of differentially expressed genes
replicates computes replicates across a vector
spectralMap Generic function to draw a spectral map, according to JnJ Standards
spectralMap,ExpressionSet,character Methods for Function spectralMap according to JnJ Standards
spectralMap-method Methods for Function spectralMap according to JnJ Standards
spectralMap-methods Methods for Function spectralMap according to JnJ Standards
topTable,fTest Methods for topTable
topTable,limma Methods for topTable
topTable,MArrayLM Methods for topTable
topTable,tTest Methods for topTable
topTable-method Methods for topTable
topTable-methods Methods for topTable
tTest Use t Test to Compare Two Groups
volcanoPlot Draw a Volcano Plot
volcanoPlot,ExpressionSet,character Methods for Function spectralMap according to JnJ Standards
volcanoPlot,limma,missing,character Draw a Volcano Plot
volcanoPlot,limma,missing,missing Draw a Volcano Plot
volcanoPlot,numeric,numeric,character Draw a Volcano Plot
volcanoPlot,numeric,numeric,missing Draw a Volcano Plot
volcanoPlot,tTest,character Draw a Volcano Plot
volcanoPlot,tTest,missing Draw a Volcano Plot
volcanoPlot-method Draw a Volcano Plot
volcanoPlot-methods Draw a Volcano Plot
volcanoplotter Workhorse function for the different volcanoPlot methods