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

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

AuthorJames W. MacDonald
Date of publicationNone
MaintainerJames W. MacDonald <jmacdon@u.washington.edu>
LicenseArtistic-2.0
Version1.46.4

View on Bioconductor

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-ExpressionSet-method: A Function to Make a PCA Plot from an ExpressionSet

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

affycoretools Man page
affycoretools-defunct Man page
affycoretools-package Man page
affyLinks Man page
affystart Man page
annBM Man page
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,character-method Man page
annotateEset,ExpressionSet,ChipDb-method Man page
annotateEset,ExpressionSet,data.frame-method Man page
dataAndHeatmapPage Man page
entrezLinks Man page
fixHeaderAndGo Man page
foldFilt Man page
foldFiltBM Man page
geneSetPage Man page
getCols Man page
getMainProbes Man page
goLinks Man page
gsHeatmap Man page
hyperG2annaffy Man page
hyperGoutput Man page
intNames Man page
limma2annaffy Man page
limma2biomaRt Man page
make.cl Man page
makeGoGeneTable Man page
makeGoTable Man page
makeHmap Man page
makeImages Man page
makeIndices Man page
makeVenn Man page
maplot Man page
mirna2mrna Man page
nuccoreLinks Man page
outputRomer Man page
pca.legend Man page
plotDeg Man page
plotHist Man page
plotPCA,ExpressionSet-method Man page
probes2table Man page
probes2tableBM Man page
runRomer Man page
tableFilt Man page
venn4Way Man page
vennCounts2 Man page
vennPage Man page
vennSelect Man page
vennSelect2 Man page
vennSelectBM Man page
vennSelectFC Man page
writeFit Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.