affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips
Version 1.48.0

Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.

AuthorJames W. MacDonald
Bioconductor views GeneExpression Microarray OneChannel ReportWriting
Date of publicationNone
MaintainerJames W. MacDonald <jmacdon@u.washington.edu>
LicenseArtistic-2.0
Version1.48.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("affycoretools")

Getting started

README.md

Popular man pages

affystart: Pre-processing for Affymetrix Data
dataAndHeatmapPage: A function to create an annotated HTML table for all genes in...
gsHeatmap: A function to create a simple heatmap and key.
makeImages: Add dotplot images
plotPCA: A Function to Make a PCA Plot from an ExpressionSet or matrix
venn4Way: 4-way Venn Diagrams
vennPage: High-level function for making Venn diagrams with clickable...
See all...

All man pages Function index File listing

Man pages

affycoretools: Make repetitive analyses of microarray and RNA-Seq data...
affycoretools-defunct: Defunct functions in package 'affycoretools'
affystart: Pre-processing for Affymetrix Data
annotateEset: Method to annotate ExpressionSets automatically
dataAndHeatmapPage: A function to create an annotated HTML table for all genes in...
entrezLinks: Add links to data when using ReportingTools
fixHeaderAndGo: Fix data.frame header for use with ReportingTools
geneSetPage: A function to create an HTML page for each gene set, as well...
getCols: Correct Ordering of Contrasts
getMainProbes: Remove control probesets from ST arrays
gsHeatmap: A function to create a simple heatmap and key.
intNames: Create Names for Venn Diagram Intersections
make.cl: A Function to Make a Classlabel Vector for Plotting
makeGoGeneTable: Make Gene table from GO analysis results
makeGoTable: Create HTML tables for Gene Ontology (GO) analyses
makeHmap: A function to create a heatmap-like object or matrix of...
makeImages: Add dotplot images
makeIndices: Create Indices for Venn Diagrams
makeVenn: High-level function for making Venn diagrams and outputting...
maplot: A Function to make MA plots from all arrays.
mirna2mrna: A function to map miRNA to mRNA.
outputRomer: A function to create HTML output from the results of running...
pca.legend: A Function to Automagically Place a Legend in a PCA Plot
plotDeg: Functions to Plot Density and RNA Degradation Plots
plotPCA: A Function to Make a PCA Plot from an ExpressionSet or matrix
runRomer: A function to run the romer function on a set of contrasts.
tableFilt: Filter a topTable object
venn4Way: 4-way Venn Diagrams
vennCounts2: Compute Counts for Venn Diagram
vennPage: High-level function for making Venn diagrams with clickable...
vennSelect2: Select and Output Genelists Based on Venn Diagrams
writeFit: Function to output annotated fit data from limma

Functions

addAnnot Source code
addLines Source code
affyLinks Man page Source code
affycoretools Man page
affycoretools-defunct Man page
affycoretools-package Man page
affystart Man page Source code
allToMat Source code
annBM Man page Source code
annotateEset Man page
annotateEset,ExpressionSet,AffyExonPDInfo-method Man page
annotateEset,ExpressionSet,AffyExpressionPDInfo-method Man page
annotateEset,ExpressionSet,AffyGenePDInfo-method Man page
annotateEset,ExpressionSet,AffyHTAPDInfo-method Man page
annotateEset,ExpressionSet,ChipDb-method Man page
annotateEset,ExpressionSet,character-method Man page
annotateEset,ExpressionSet,data.frame-method Man page
colvec Source code
convertIDs Source code
dataAndHeatmapPage Man page Source code
dataFromNetaffx Source code
drawVenn Source code
ensemblLinks Man page Source code
entrezLinks Man page Source code
fixHeaderAndGo Man page Source code
foldFilt Man page Source code
foldFiltBM Man page Source code
geneSetPage Man page Source code
getCols Man page Source code
getMainProbes Man page Source code
goLinks Man page Source code
gsHeatmap Man page Source code
hyperG2annaffy Man page Source code
hyperGoutput Man page Source code
intNames Man page Source code
limma2annaffy Man page Source code
limma2biomaRt Man page Source code
listToVector Source code
make.cl Man page Source code
makeFullDf Source code
makeGenePlots Source code
makeGoGeneTable Man page Source code
makeGoTable Man page Source code
makeHmap Man page Source code
makeImages Man page Source code
makeIndices Man page Source code
makeVenn Man page
makeVenn,DGEGLM-method Man page
makeVenn,MArrayLM-method Man page
maplot Man page Source code
mirna2mrna Man page Source code
nuccoreLinks Man page Source code
onLoad Source code
outPut Source code
outputRomer Man page Source code
pca.legend Man page Source code
pcaPCH Source code
plotDeg Man page Source code
plotHist Man page Source code
plotPCA Man page
plotPCA,ExpressionSet-method Man page
plotPCA,matrix-method Man page
probes2table Man page Source code
probes2tableBM Man page Source code
queryMaker Source code
remove.axis.and.padding Source code
runRomer Man page Source code
tableFilt Man page Source code
venn4Way Man page Source code
vennCounts2 Man page Source code
vennLinks Source code
vennPage Man page Source code
vennSelect Man page Source code
vennSelect2 Man page Source code
vennSelectBM Man page Source code
vennSelectFC Man page Source code
whichMains Source code
writeFit Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllGenerics.R
R/Defunct.R
R/affycoretools.R
R/affystart.R
R/annotateEset.R
R/geneSetTables.R
R/mirnaFuns.R
R/plotma.R
R/reportingTools.R
R/vennSelect.R
R/zzz.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/RefactoredAffycoretools.R
inst/doc/RefactoredAffycoretools.Rnw
inst/doc/RefactoredAffycoretools.pdf
inst/examples
inst/examples/Statistical_analysis.Rnw
inst/examples/Statistical_analysis.bib
man
man/affycoretools-defunct.Rd
man/affycoretools.Rd
man/affystart.Rd
man/annotateEset.Rd
man/dataAndHeatmapPage.Rd
man/entrezLinks.Rd
man/fixHeaderAndGo.Rd
man/geneSetPage.Rd
man/getCols.Rd
man/getMainProbes.Rd
man/gsHeatmap.Rd
man/intNames.Rd
man/make.cl.Rd
man/makeGoGeneTable.Rd
man/makeGoTable.Rd
man/makeHmap.Rd
man/makeImages.Rd
man/makeIndices.Rd
man/makeVenn.Rd
man/maplot.Rd
man/mirna2mrna.Rd
man/outputRomer.Rd
man/pca.legend.Rd
man/plotDeg.Rd
man/plotPCA.Rd
man/runRomer.Rd
man/tableFilt.Rd
man/venn4Way.Rd
man/vennCounts2.Rd
man/vennPage.Rd
man/vennSelect2.Rd
man/writeFit.Rd
vignettes
vignettes/RefactoredAffycoretools.Rnw
vignettes/abatch.Rdata
vignettes/exprSet.Rdata
vignettes/exprSet2.Rdata
vignettes/pdata.txt
affycoretools documentation built on May 20, 2017, 9:17 p.m.

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