View source: R/enrichment_functions.R
extractPvalues | R Documentation |
This function reshapes the output from multiGSEA to get a single data frame with columns for p-values and adjusted p-values for each omics layer. Each row of the data frame represents one pathway.
extractPvalues(enrichmentScores, pathwayNames)
enrichmentScores |
Nested List of enrichment scores, calculated by multiGSEA function. |
pathwayNames |
List containing Pathway names. |
Data frame where rows are pathways and columns are (adjusted) p-values for each 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 es <- multiGSEA(pathways, ranks) extractPvalues( enrichmentScores = es, pathwayNames = names(pathways[[1]]) )
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.