DEXSeqHTML: DEXSeq HTML report writer

Description Usage Arguments Value Examples

View source: R/htmlReports.R

Description

This function generates an HTML report from the results of a DEXSeqResults object. Gives an simple report to explore differential exon usage results.

Usage

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  DEXSeqHTML(object, genes=NULL, path="DEXSeqReport", file="testForDEU.html", 
    fitExpToVar="condition", FDR=0.1, color=NULL, color.samples=NULL,
    mart="", filter="", attributes="", extraCols=NULL, BPPARAM=MulticoreParam(workers=1))

Arguments

object

An DEXSeqResults object

genes

A character vector of gene identifiers to be included in the report. If 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.

FDR

A false discovery rate

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 DEXSeqResults 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.

BPPARAM

A 'BiocParallelParam' instance. See ?bplapply for details.

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)

Examples

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  ## Not run: 
    data(pasillaDEXSeqDataSet, package="pasilla")
    dxr <- DEXSeq( dxd )
    DEXSeqHTML( object=dxr )
  
## End(Not run)

areyesq89/DEXSeq documentation built on June 26, 2020, 2:31 a.m.