gsea2html {phenoTest} | R Documentation

## Export an object of class gseaData to an html file.

### Description

Exports `gseaData` objects to html files with plots and links to online databases.

### Usage

    gsea2html(gseaData, epheno, variable, title = "", path, file, digits = 3, plotEs = FALSE, limit=100)

### Arguments

`gseaData` | an object of class `gseaData`.
`epheno` | the object of class `epheno` that was used to create `gseaData`.
`variable` | varible that we are interested in.
`title` | title that will be shown on top of the table.
`path` | directory where we want to store the html files.
`file` | filename.
`digits` | Number of decimal digits that will be shown on the table.
`plotEs` | if this is TRUE enrichment score plots will be plotted instead of normalized enrichment score plots.
`limit` | maximum number of gene sets that will be exported.

### Details

This function produces a browseable version of the table that we can obtain with `summary(gseaData)`. We will obtain one plot per NES (or ES) and we will be able to see which genes belong to each gene set and the values they have in the `epheno` object.

### Author(s)

Evarist Planet

### Examples

    #WITH PROBESET AS IDENTIFIER
    data(eset)
    data(epheno)

    set.seed(777)
    sign1 <- sample(featureNames(eset))[1:20]
    sign2 <- sample(featureNames(eset))[1:50]
    mySignature <- list(sign1,sign2)
    names(mySignature) <- c('My first signature','Another signature')
    mySignature

    mygsea <- gsea(x=epheno[,1],gsets=mySignature,B=100,p.adjust='BH')
    summary(mygsea)

    #following line has been commented to prevent the creation of files
    #gsea2html(gseaData=mygsea,epheno=epheno,variable=phenoNames(epheno)[1],title='My test',path='~/Desktop',file='myGSEA.html')

    #WITH ENTREZID AS IDENTIFIER
    data(eset.genelevel)
    eset.genelevel

    set.seed(777)
    sign1 <- sample(featureNames(eset.genelevel))[1:20]
    sign2 <- sample(featureNames(eset.genelevel))[1:50]
    mySignature.genelevel <- list(sign1,sign2)
    names(mySignature.genelevel) <- c('My first signature','Another signature')
    mySignature.genelevel

    epheno.genelevel <- ExpressionPhenoTest(eset.genelevel,vars2test=list(categorical='lymph.node.status'))
    mygsea.genelevel <- gsea(x=epheno.genelevel,gsets=mySignature.genelevel,B=100,p.adjust='BH')
    summary(mygsea.genelevel)

    #following line has been commented to prevent the creation of files
    #gsea2html(gseaData=mygsea.genelevel,epheno=epheno.genelevel,variable=phenoNames(epheno.genelevel),title='My test (at genelevel)',path='~/Desktop',file='myGSEA_genelevel.html')

[Package phenoTest version 1.35.1 Index]