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a4Base (version 1.20.0)
Automated Affymetrix Array Analysis Base Package
Description
Automated Affymetrix Array Analysis
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Version
1.20.0
1.18.0
1.16.0
1.14.0
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Version
1.20.0
License
GPL-3
Maintainer
Tobias Verbeke
Last Published
October 2nd, 2013
Functions in a4Base (1.20.0)
Search functions
replicates
computes replicates across a vector
limmaTwoLevels
Wrapper function for the comparison of two groups using limma
computeLogRatio
Summary statistics for gene expression
combineTwoExpressionSet
Combine two ExpressionSet objects
ExpressionSetWithComputation-class
Class "ExpressionSetWithComputation"
addQuantilesColors
Compute quantiles for plotGeneDE function
nlcvTT
Data to Demonstrate nlcv and Co Functions
plotCombination2genes
Plot a Combination of Two Genes
histpvalueplotter
Workhorse function for the histPvalue function
createExpressionSet
combine gene expression and phenotype data onto a ExpressionSet object
boxPlot
Create a boxplot for a given gene.
volcanoplotter
Workhorse function for the different volcanoPlot methods
logReg
Logistic regression for predicting the probability to belong to a certain class in binary classification problems.
spectralMap-methods
Methods for Function spectralMap
plotCombMultSamples
Plots the correlation in gene expression between more than 2 samples
probe2gene
Translate Affymetrix probeset IDs into gene symbols
plotComb2Samples
Plots the correlation in gene expression between two samples
filterVarInt
Filter Features On Intensity and Variance
plotLogRatio
Plot a summary gene expression graph
propDEgenes
Generic function to compute the proportion of differentially expressed genes that are present
lassoReg
Multiple regression using the Lasso algorithm as implemented in the glmnet package
probabilitiesPlot
Function to plot the probabilities to belong to a certain class in binary classification problems.
volcanoPlot
Draw a Volcano Plot
propdegenescalculation
Estimation of proportion of differentially expressed genes
profilesPlot
Plot expression profiles of multiple genes or probesets
volcanoPlot-methods
Draw a Volcano Plot
heatmap.expressionSet
Image plot of an expressionSet
histPvalue
Plot the Distribution of P Values
tTest
Use t Test to Compare Two Groups
topTable-methods
Methods for topTable
plot1gene
Create a Profile Plot for a given Gene
spectralMap
Draw a Spectral Map
a4palette
Utility function that defines a color palette for use in a4
propDEgenes-methods
Methods for propDEgenes