gsea2html: Export an object of class gseaData to an html file.

In phenoTest: Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.

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')

phenoTest documentation built on Nov. 8, 2020, 7:53 p.m.