a4 package - RDocumentation

profilesPlot

Plot expression profiles of multiple genes or probesets

probe2gene

Translate Affymetrix probeset IDs into gene symbols

volcanoPlot

Draw a Volcano Plot

rfClass

Classify using Random Forests

spectralMap

Draw a Spectral Map

ExpressionSetWithComputation-class

Class "ExpressionSetWithComputation"

addGeneInfo

Utility Function to Add Annotation to existing ExpressionSet Objects

boxPlot

Create a boxplot for a given gene.

combineTwoExpressionSet

Combine two ExpressionSet objects

generateGOIdLinks

Transform a GO ID into a hyperlink

a4palette

Utility function that defines a color palette for use in a4

createExpressionSet

combine gene expression and phenotype data onto a ExpressionSet object

limmaTwoLevels

Wrapper function for the comparison of two groups using limma

plotComb2Samples

Plots the correlation in gene expression between two samples

histpvalueplotter

Workhorse function for the histPvalue function

nlcvTT

Data to Demonstrate nlcv and Co Functions

probabilitiesPlot

Function to plot the probabilities to belong to a certain class in binary classification problems.

plot1gene

Create a Profile Plot for a given Gene

computeLogRatio

Summary statistics for gene expression

topTable-methods

Methods for topTable

plotLogRatio

Plot a summary gene expression graph

replicates

computes replicates across a vector

ROCcurve

Receiver operating curve

annotationTable

Function to Create an annotationTable

topTable

S4 Generic for obtaining a top table

generateEntrezIdLinks

Transform an ENTREZ ID into a hyperlink

simulateData

Simulate Data for Package Testing and Demonstration Purposes

addQuantilesColors

Compute quantiles for plotGeneDE function

logReg

Logistic regression for predicting the probability to belong to a certain class in binary classification problems.

xtable-methods

Methods for Function xtable in Package `annotationTable'

histPvalue

Plot the Distribution of P Values

lassoReg

Multiple regression using the Lasso algorithm as implemented in the glmnet package

plotCombMultSamples

Plots the correlation in gene expression between more than 2 samples

volcanoPlot-methods

Draw a Volcano Plot

propDEgenes-methods

Methods for propDEgenes

print.xtableAnnotationTable

Print method for 'xtableAnnotationTable' objects

confusionMatrix

Generic function to produce a confusion matrix (related to a classification problem)

volcanoplotter

Workhorse function for the different volcanoPlot methods

propDEgenes

Generic function to compute the proportion of differentially expressed genes that are present

pamClass

Classify using Prediction Analysis for MicroArrays

heatmap.expressionSet

Image plot of an expressionSet

spectralMap-methods

Methods for Function spectralMap

propdegenescalculation

Estimation of proportion of differentially expressed genes

plotCombination2genes

Plot a Combination of Two Genes

lassoClass

Classify using the Lasso

filterVarInt

Filter Features On Intensity and Variance

tTest

Use t Test to Compare Two Groups

annotationTable-class

Class "annotationTable"

a4 (version 1.20.0)

Automated Affymetrix Array Analysis Umbrella Package

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Functions in a4 (1.20.0)