View source: R/findPathClusters.R
findPathClusters | R Documentation |
Calculates the clusters within the enrichment data based on pathway similarity.
findPathClusters(enrichment, methods = aPEAR.methods, verbose = FALSE, ...)
enrichment |
a data.frame containing enrichment results |
methods |
methods for calculating the pathway clusters within the enrichment result (object of class aPEAR.methods; default: aPEAR.methods) |
verbose |
enable / disable log messages (default: FALSE) |
... |
additional parameters (see |
a list of two objects: sim
- pathway similarity matrix; and
clusters
- pathway clusters
a list of clusters and similarity matrix
# Load libraries
library(clusterProfiler)
library(DOSE)
library(org.Hs.eg.db)
data(geneList)
# Perform enrichment using clusterProfiler
enrich <- gseGO(geneList, OrgDb = org.Hs.eg.db, ont = 'CC')
# Obtain clusters within the enriched pathways using default parameters
data <- findPathClusters(enrich@result)
data$clusters
# Obtain clusters within the enriched pathways using hierarchical clustering
# and minClusterSize = 1
data <- findPathClusters(enrich@result, cluster = 'hier', minClusterSize = 1)
data$clusters
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