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a4Base (version 1.14.0)

Automated Affymetrix Array Analysis Base Package

Description

Automated Affymetrix Array Analysis

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Version

Version

1.14.0

License

GPL-3

Maintainer

Tobias Verbeke

Last Published

February 15th, 2017

Functions in a4Base (1.14.0)

ExpressionSetWithComputation-class

Class "ExpressionSetWithComputation"
histPvalue

Plot the Distribution of P Values
addQuantilesColors

Compute quantiles for plotGeneDE function
boxPlot

Create a boxplot for a given gene.
combineTwoExpressionSet

Combine two ExpressionSet objects
createExpressionSet

combine gene expression and phenotype data onto a ExpressionSet object
a4palette

Utility function that defines a color palette for use in a4
heatmap.expressionSet

Image plot of an expressionSet
filterVarInt

Filter Features On Intensity and Variance
computeLogRatio

Summary statistics for gene expression
plotCombination2genes

Plot a Combination of Two Genes
plot1gene

Create a Profile Plot for a given Gene
limmaTwoLevels

Wrapper function for the comparison of two groups using limma
logReg

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

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

Workhorse function for the histPvalue function
plotCombMultSamples

Plots the correlation in gene expression between more than 2 samples
plotLogRatio

Plot a summary gene expression graph
nlcvTT

Data to Demonstrate nlcv and Co Functions
plotComb2Samples

Plots the correlation in gene expression between two samples
probabilitiesPlot

Function to plot the probabilities to belong to a certain class in binary classification problems.
probe2gene

Translate Affymetrix probeset IDs into gene symbols
propDEgenes

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

computes replicates across a vector
propDEgenes-methods

Methods for propDEgenes
propdegenescalculation

Estimation of proportion of differentially expressed genes
spectralMap

Draw a Spectral Map
topTable-methods

Methods for topTable
spectralMap-methods

Methods for Function spectralMap
profilesPlot

Plot expression profiles of multiple genes or probesets
volcanoplotter

Workhorse function for the different volcanoPlot methods
tTest

Use t Test to Compare Two Groups
volcanoPlot-methods

Draw a Volcano Plot
volcanoPlot

Draw a Volcano Plot