Package: a4Base 1.53.0

Laure Cougnaud

a4Base: Automated Affymetrix Array Analysis Base Package

Base utility functions are available for the Automated Affymetrix Array Analysis set of packages.

Authors:Willem Talloen [aut], Tine Casneuf [aut], An De Bondt [aut], Steven Osselaer [aut], Hinrich Goehlmann [aut], Willem Ligtenberg [aut], Tobias Verbeke [aut], Laure Cougnaud [cre]

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a4Base.pdf |a4Base.html✨
a4Base/json (API)
NEWS

# Install 'a4Base' in R:
install.packages('a4Base', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • nlcvTT - Data to Demonstrate nlcv and Co Functions

On BioConductor:a4Base-1.53.0(bioc 3.20)a4Base-1.52.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

29 exports 1.38 score 69 dependencies 1 dependents

Last updated 2 months agofrom:7a868d362d

Exports:a4paletteaddQuantilesColorsboxPlotcombineTwoExpressionSetcomputeLogRatiocreateExpressionSetfilterVarIntheatmap.expressionSethistPvaluehistpvalueplotterlassoReglimmaTwoLevelslogRegplot1geneplotComb2SamplesplotCombination2genesplotCombMultSamplesplotLogRatioprobabilitiesPlotprobe2geneprofilesPlotpropDEgenespropdegenescalculationreplicatesspectralMaptopTabletTestvolcanoPlotvolcanoplotter

Dependencies:a4Corea4PreprocannaffyannotateAnnotationDbiaskpassBiobaseBiocGenericsBiocManagerBiostringsbitbit64bitopsblobcachemcaToolsclicodetoolscpp11crayoncurlDBIfastmapforeachgenefilterGenomeInfoDbGenomeInfoDbDataglmnetglueGO.dbgplotsgtoolshttrIRangesiteratorsjsonliteKEGGRESTKernSmoothlatticelifecyclelimmaMASSMatrixMatrixGenericsmatrixStatsmemoisemimempmmulttestopensslpkgconfigplogrpngR6RcppRcppEigenrlangRSQLiteS4VectorsshapestatmodsurvivalsysUCSC.utilsvctrsXMLxtableXVectorzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Utility function that defines a color palette for use in a4a4palette
Compute quantiles for plotGeneDE functionaddQuantilesColors
Create a boxplot for a given gene.boxPlot
Combine two ExpressionSet objectscombineTwoExpressionSet
Summary statistics for gene expressioncomputeLogRatio
combine gene expression and phenotype data onto a ExpressionSet objectcreateExpressionSet
Class "ExpressionSetWithComputation"ExpressionSetWithComputation-class
Filtering on Intensity and VariancefilterVarInt
Image plot of an expressionSetheatmap.expressionSet
Plot the Distribution of P ValueshistPvalue histPvalue,limma-method histPvalue,MArrayLM-method histPvalue,numeric-method
Workhorse function for the histPvalue functionhistpvalueplotter
Multiple regression using the Lasso algorithm as implemented in the glmnet packagelassoReg
Wrapper for the limma function for the comparison of two groups (two factor levels)limmaReg
Wrapper for the limma function for the comparison of two groups (two factor levels)limmaTwoLevels
Logistic regression for predicting the probability to belong to a certain class in binary classification problemslogReg
Data to Demonstrate nlcv and Co FunctionsnlcvTT
Pick One or More OA ColorsoaColors
Generate a Palette of OA ColorsoaPalette
Create a Profile Plot for a given Geneplot1gene
Plots the correlation in gene expression between two samplesplotComb2Samples
Plot a Combination of Two GenesplotCombination2genes
Plots the correlation in gene expression between more than 2 samplesplotCombMultSamples
Plot a summary gene expression graphplotLogRatio
Function to plot the probabilities to belong to a certain class in binary classification problems.probabilitiesPlot
Translate Affymetrix probeset IDs into gene symbolsprobe2gene
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.profilesPlot
Generic function to compute the proportion of differentially expressed genes that are presentpropDEgenes
Generic function to compute the proportion of differentially expressed genes that are presentpropDEgenes,limma propDEgenes,limma-method propDEgenes,numeric propDEgenes,numeric-method propDEgenes-methods
Estimation of proportion of differentially expressed genespropdegenescalculation
computes replicates across a vectorreplicates
Generic function to draw a spectral map, according to JnJ StandardsspectralMap
Methods for Function spectralMap according to JnJ StandardsspectralMap,ExpressionSet,character spectralMap,ExpressionSet,character-method spectralMap-methods volcanoPlot,ExpressionSet,character
Methods for topTabletopTable,fTest topTable,fTest-method topTable,limma topTable,limma-method topTable,MArrayLM topTable,MArrayLM-method topTable,tTest topTable,tTest-method topTable-methods
Use t Test to Compare Two GroupstTest
Draw a Volcano PlotvolcanoPlot
Draw a Volcano PlotvolcanoPlot,limma,missing,character volcanoPlot,limma,missing,character-method volcanoPlot,limma,missing,missing volcanoPlot,limma,missing,missing-method volcanoPlot,numeric,numeric,character volcanoPlot,numeric,numeric,character-method volcanoPlot,numeric,numeric,missing volcanoPlot,numeric,numeric,missing-method volcanoPlot,tTest,character volcanoPlot,tTest,missing volcanoPlot,tTest,missing,character-method volcanoPlot,tTest,missing,missing-method volcanoPlot-methods
Workhorse function for the different volcanoPlot methodsvolcanoplotter