phenoTest (version 1.20.0)

gsea2html: 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.

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')