R: HTML report writer

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,
     mart="", filter="", attributes="", extraCols=NULL, nCores=1)

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.
`mart`	object of class Mart, created with the useMart function, with dataset specified
`filter`	Filters (ONLY ONE) that should be used in the query. A possible list of filters can be retrieved using the function listFilters. Please note that the value of this filter will always be the geneIDs in the ExonCountSet object.
`attributes`	Attributes you want to retrieve. A possible list of attributes can be retrieved using the biomaRt function listAttributes.
`extraCols`	A data frame with one or more columns to add to the report. For example, additional information about the genes. The data frame should be indexed by the gene names of the ExonCountSet object, e.g. the rownames of the data frame should correspond to the gene names.
`nCores`	Number of cores to be used. The `parallel` package must be loaded in order to spread the job onto several cores.

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 SVG files with the plots and other html files are placed. Different plots with different labels are generated for each gene: - counts: the raw data, for each sample - fitted expression: the fitted coefficients per compared condition (e.g.: treated, untreated) - fitted splicing: as 'expression', but after removing overall gene-level differential expression: this is the view most relevant for the interpretation of DEXSeq results, which are about changes in relative exon usage (i.e.: relative to overall gene expression)

To see an example please visit http://www-huber.embl.de/pub/DEXSeq/psfb/testForDEU.html.

Examples

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