clusters

Performs clustering of SNN graph of genesets.

# S3 method for BOWER
find_clusters(bower, resolution = 3, ...)

# S3 method for igraph
find_clusters(gr, resolution = 3, ...)

Arguments

bower	BOWER class..
resolution	value for leiden clustering.
...	passed to leiden::leiden.
gr	igraph object.

Value

Cluster assignment for each geneset.

Examples

gmt_file <- system.file("extdata", "h.all.v7.4.symbols.gmt", package = "bowerbird")
bwr <- bower(gmt_file)
bwr <- snn_graph(bwr)
bwr <- find_clusters(bwr)
bwr
#> BOWER class
#> number of genesets:  50 
#> genesets kNN Graph: 
#> IGRAPH 8d29876 UNW- 50 124 -- 
#> + attr: name (v/c), cluster (v/n), geneset_size (v/n), weight (e/n)
#> + edges from 8d29876 (vertex names):
#> [1] HALLMARK_TNFA_SIGNALING_VIA_NFKB--HALLMARK_HYPOXIA                          
#> [2] HALLMARK_TNFA_SIGNALING_VIA_NFKB--HALLMARK_TGF_BETA_SIGNALING               
#> [3] HALLMARK_TNFA_SIGNALING_VIA_NFKB--HALLMARK_IL6_JAK_STAT3_SIGNALING          
#> [4] HALLMARK_TNFA_SIGNALING_VIA_NFKB--HALLMARK_APOPTOSIS                        
#> [5] HALLMARK_TNFA_SIGNALING_VIA_NFKB--HALLMARK_MYOGENESIS                       
#> [6] HALLMARK_TNFA_SIGNALING_VIA_NFKB--HALLMARK_COMPLEMENT                       
#> [7] HALLMARK_TNFA_SIGNALING_VIA_NFKB--HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION
#> + ... omitted several edges
#> number of geneset clusters:  10