Package: a4Base 1.55.0

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'))

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.

microarray

2.92 score 1 packages 14 scripts 441 downloads 29 exports 69 dependencies

Last updated 25 days agofrom:d78b7ffab9. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 30 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 30 2024
R-4.4-mac	NOTE	Oct 30 2024
R-4.3-win	NOTE	Oct 30 2024
R-4.3-mac	NOTE	Oct 30 2024

Exports:a4palette addQuantilesColors boxPlot combineTwoExpressionSet computeLogRatio createExpressionSet filterVarInt heatmap.expressionSet histPvalue histpvalueplotter lassoReg limmaTwoLevels logReg plot1gene plotComb2Samples plotCombination2genes plotCombMultSamples plotLogRatio probabilitiesPlot probe2gene profilesPlot propDEgenes propdegenescalculation replicates spectralMap topTable tTest volcanoPlot volcanoplotter

Dependencies:a4Core a4Preproc annaffy annotate AnnotationDbi askpass Biobase BiocGenerics BiocManager Biostrings bit bit64 bitops blob cachem caTools cli codetools cpp11 crayon curl DBI fastmap foreach genefilter GenomeInfoDb GenomeInfoDbData glmnet glue GO.db gplots gtools httr IRanges iterators jsonlite KEGGREST KernSmooth lattice lifecycle limma MASS Matrix MatrixGenerics matrixStats memoise mime mpm multtest openssl pkgconfig plogr png R6 Rcpp RcppEigen rlang RSQLite S4Vectors shape statmod survival sys UCSC.utils vctrs XML xtable XVector zlibbioc

Citation

Development and contributors

Readme and manuals

Help Manual

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