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affycoretools

Make repetitive analyses of microarray and RNA-Seq data simpler with affycoretools.

The affycoretools package is primarily intended to make analyses of Affymetrix GeneChip data simpler and more straightforward. There are any number of packages designed for preprocessing or analyzing Affy data, but there are not so many that help streamline the analysis to help create useful output that can be given to collaborators.

The affycoretools package is also intended to be used as a way to do reproducible research, where the analysis and documentation are all held in a single file, that is then processed by R to create the output data, as well as a nicely formatted pdf that documents the analysis. The affycoretools package can be used with either Sweave or knitr documents, although these days knitr is really the way to go.

In addition, affycoretools can be used with either annaffy or ReportingTools to create useful output in HTML or text format to share with your collaborators. However, ReportingTools is being actively developed and maintained, whereas annaffy is not, so the intention is to slowly convert all the functions to primarily use ReportingTools.

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Version

Version

1.38.0

License

Artistic-2.0

Maintainer

James W MacDonald

Last Published

February 15th, 2017

Functions in affycoretools (1.38.0)

Add dotplot images

Create Indices for Venn Diagrams

Function to output annotated fit data from limma

A Function to make MA plots from all arrays.

High-level function for making Venn diagrams and outputting the results from the diagrams in HTML and CSV files.

Select Available Annotation from a Biomart

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.

Output Tables Based on Hypergeometric Test

HTML tables from GOIDs

Function to Create HTML Tables from limma Objects using biomaRt for Annotation

Extract Statistics from an MArrayLM object

Add links to data when using ReportingTools

Interactive Functions for limma2anaffy

Create HTML tables for Gene Ontology (GO) analyses

Correct Ordering of Contrasts

A function to create a heatmap-like object or matrix of correlations between miRNA and mRNA data.

A function to run the romer function on a set of contrasts.

Convert Affy Probe ids to Annotated HTML Table using biomaRt

Select and Output Gene Lists Based on Venn Diagrams

Select and Output Genelists Based on Venn Diagrams using biomaRt

A Function to Make a PCA Plot from an ExpressionSet

A Function to Make a Classlabel Vector for Plotting

Convert Affy Probe ids to Annotated HTML Table

Make repetitive analyses of microarray and RNA-Seq data simpler with affycoretools.

A function to create a simple heatmap and key.

Internal functions for hyperGoutput

Pre-processing for Affymetrix Data

Create Names for Venn Diagram Intersections

Function to Create HTML Tables from limma Objects

A function to map miRNA to mRNA.

A function to create HTML output from the results of running romer on a set of contrasts.

Select and Output Genelists Based on Venn Diagrams

Select and Output Genelists Based on Venn Diagrams

Fix data.frame header for use with ReportingTools

Output Fold Change Data

Subset a Vector of Probesets

Order Probesets Based on Fold Change Values

Make a Fold Change List

makeGoGeneTable

Make Gene table from GO analysis results

Compute Counts for Venn Diagram

High-level function for making Venn diagrams with clickable links to HTML pages with the underlying genes.

Output Fold Change Data using biomaRt

A function to create an HTML page for each gene set, as well as the HTML pages for each significant gene set.

Remove control probesets from ST arrays

A Function to Automagically Place a Legend in a PCA Plot

Functions to Plot Density and RNA Degradation Plots

Filter a topTable object

4-way Venn Diagrams