distill_enrichment {GeneTonic} | R Documentation |
Distill the main topics from the enrichment results, based on the graph derived from constructing an enrichment map
distill_enrichment( res_enrich, res_de, annotation_obj, n_gs = nrow(res_enrich), cluster_fun = "cluster_markov" )
res_enrich |
A |
res_de |
A |
annotation_obj |
A |
n_gs |
Integer value, corresponding to the maximal number of gene sets to be used. |
cluster_fun |
Character, referring to the name of the function used for
the community detection in the enrichment map graph. Could be one of "cluster_markov",
"cluster_louvain", or "cluster_walktrap", as they all return a |
A list containing three objects:
the distilled table of enrichment, distilled_table
, where the new meta-genesets
are identified and defined, specifying e.g. the names of each component, and the
genes associated to these.
the distilled graph for the enrichment map, distilled_em
, with the information
on the membership
the original res_enrich
, augmented with the information of the membership
related to the meta-genesets
library("macrophage") library("DESeq2") library("org.Hs.eg.db") library("AnnotationDbi") # dds object data("gse", package = "macrophage") dds_macrophage <- DESeqDataSet(gse, design = ~line + condition) rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15) dds_macrophage <- estimateSizeFactors(dds_macrophage) # annotation object anno_df <- data.frame( gene_id = rownames(dds_macrophage), gene_name = mapIds(org.Hs.eg.db, keys = rownames(dds_macrophage), column = "SYMBOL", keytype = "ENSEMBL"), stringsAsFactors = FALSE, row.names = rownames(dds_macrophage) ) # res object data(res_de_macrophage, package = "GeneTonic") res_de <- res_macrophage_IFNg_vs_naive # res_enrich object data(res_enrich_macrophage, package = "GeneTonic") res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive) res_enrich <- get_aggrscores(res_enrich, res_de, anno_df) distilled <- distill_enrichment(res_enrich, res_de, annotation_obj, n_gs = 100, cluster_fun = "cluster_markov") colnames(distilled$distilled_table) distilled$distilled_em