This function calculates GSEA-based enrichments scores for multiple omics
layer at once. Input pathways or gene sets have to be prepared in advance by
means of the function
initOmicsDataStructure. The function uses pre-
ranked lists for each omics layer to calculate the enrichment score. The
ranking can be calculated by means of the function
Nested list containing all pathway features for the respective omics layer.
Nested list containing the measured and pre-ranked features for each omics layer.
Nested list containing the enrichment scores for each given pathway and omics layer.
# Download pathway definition and extract features pathways <- getMultiOmicsFeatures(dbs = c("kegg"), layer = c("transcriptome", "proteome")) # load omics data and calculate ranks data(transcriptome) data(proteome) ranks <- initOmicsDataStructure(c("transcriptome", "proteome")) ranks$transcriptome <- rankFeatures(transcriptome$logFC, transcriptome$pValue) names(ranks$transcriptome) <- transcriptome$Symbol ranks$proteome <- rankFeatures(proteome$logFC, proteome$pValue) names(ranks$proteome) <- proteome$Symbol ## run the enrichment multiGSEA(pathways, ranks)
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