DEXSeqHTML {DEXSeq}R Documentation

HTML report writer

Description

This function generates an HTML report from the results from testForDEU saved in an ExonCountSet object. It uses the information from the function DEUresultTable and plotting from plotDEXSeq. This gives an easy way of exploring the results of the tests.

Usage

DEXSeqHTML(ecs, geneIDs=NULL, path="DEXSeqReport", file="testForDEU.html", 
     fitExpToVar="condition", FDR=0.1, color=NULL, color.samples=NULL)
     

Arguments

ecs

An ExonCountSet object

geneIDs

A character vector of gene identificators to be included in the report. If left NULL, the genes included in the report will be the significant hits at the given false discovery rate. See "FDR" below.

path

A path in the system where to write the report.

file

The name of the html file.

fitExpToVar

A variable contained in the design of the ecs; the counts will be fitted to this variable to get the plotting values. (See plotDEXSeq for details.

FDR

A false discovery rate for the result.

color

A vector of colors, one for each of the levels of the values of "fitExpToVar".

color.samples

A vector of colors for each of the samples. If NULL, the colors of each sample will be asigned according to its corresponding condition. Useful to visualize complex experimental designs.

Value

This function will write an HTML report in the directory specified by 'path'. There, it will create an html file with the initial report page and a directory called "files" in which SCG files with the plots and other html files are placed. To see an example please visit http://www.embl.de/~reyes/DEXSeqReport/testForDEU.html.

See Also

hwrite

Examples

	## Not run: 
           data("pasillaExons", package="pasilla")
           pasillaExons <- estimateSizeFactors( pasillaExons )
           pasillaExons <- estimateDispersions( pasillaExons )
           pasillaExons <- fitDispersionFunction( pasillaExons )
           pasillaExons <- testForDEU( pasillaExons )
           DEXSeqHTML( pasillaExons )
        
## End(Not run)
     

[Package DEXSeq version 1.0.2 Index]