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
multiGSEA(pathways, ranks, eps = 0)
Nested list containing all pathway features for the respective omics layer.
Nested list containing the measured and pre-ranked features for each omics layer.
This parameter sets the boundary for calculating the p value.
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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