gsea2html {phenoTest} | R Documentation |
Exports gseaData
objects to html files with plots and links to online databases.
gsea2html(gseaData, epheno, variable, title = "", path, file, digits = 3, plotEs = FALSE, limit=100)
gseaData |
an object of class |
epheno |
the object of class |
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. |
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.
Evarist Planet
#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')