Functions useful for those doing repetitive analyses with Affymetrix GeneChips

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Documentation for package ‘affycoretools’ version 1.70.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

affycoretools	Make repetitive analyses of microarray and RNA-Seq data simpler with affycoretools.
affyLinks	Add links to data when using ReportingTools
affystart	Pre-processing for Affymetrix Data
annotateEset	Method to annotate ExpressionSets automatically
annotateEset-method	Method to annotate ExpressionSets automatically
dataAndHeatmapPage	A function to create an annotated HTML table for all genes in a significant gene set as well as a heatmap of these data.
doGlimma	A function to generate MA-plots from Glimma, for all contrasts.
ensemblLinks	Add links to data when using ReportingTools
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 as the HTML pages for each significant gene set.
getMainProbes	Remove control probesets from ST arrays
goLinks	Add links to data when using ReportingTools
gsHeatmap	A function to create a simple heatmap and key.
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 correlations between miRNA and mRNA data.
makeImages	Add dotplot images
makeVenn	High-level function for making Venn diagrams and outputting the results from the diagrams in HTML and CSV files.
makeVenn-method	High-level function for making Venn diagrams and outputting the results from the diagrams in HTML and CSV files.
maplot	A Function to make MA plots from all arrays.
mirna2mrna	A function to map miRNA to mRNA.
nuccoreLinks	Add links to data when using ReportingTools
outputRomer	A function to create HTML output from the results of running romer on a set of contrasts.
outputRomer-method	A function to create HTML output from the results of running romer on a set of contrasts.
plotDeg	Functions to Plot Density and RNA Degradation Plots
plotHist	Functions to Plot Density and RNA Degradation Plots
plotPCA	A Function to Make a PCA Plot from an ExpressionSet or matrix
plotPCA-method	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.
runRomer-method	A function to run the romer function on a set of contrasts.
venn4Way	4-way Venn Diagrams
vennCounts2	Compute Counts for Venn Diagram
vennInLine	Generate Venn diagrams with links for Rmarkdown documents
vennPage	High-level function for making Venn diagrams with clickable links to HTML pages with the underlying genes.
vennSelect2	Select and Output Genelists Based on Venn Diagrams
writeFit	Function to output annotated fit data from limma