extract_core.RdSummarize the outersection genes for the. summary terms.
# S3 method for BOWER extract_core(bower, inplace = TRUE)
| bower | processed bower object. |
|---|---|
| inplace | whether or not to return an updated BOWER class or return the output as a list. |
Returns a list of genes that outersect geneset clusters in coregenes slot or as a list.
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 <- summarize_clusters(bwr, ncpus = 1) extract_core(bwr) #> BOWER class #> number of genesets: 50 #> genesets kNN Graph: #> IGRAPH 8d33b2e UNW- 50 124 -- #> + attr: name (v/c), cluster (v/n), geneset_size (v/n), terms (v/c), #> | labels (v/c), weight (e/n) #> + edges from 8d33b2e (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 #> + ... omitted several edges #> number of geneset clusters: 9 #> Core genes: #> First six genes shown #> XENOBIOTIC METABOLISM : LIFR DNAJB9 CD36 ACOX1 IDH1 ECH1 ... #> E2F TARGETS : SAC3D1 KIF11 KIF23 RACGAP1 NUMA1 KIF2C ... #> ESTROGEN RESPONSE EARLY : JAG1 CTNNB1 GNAI1 FDFT1 DHCR7 FASN ... #> INTERFERON ALPHA RESPONSE : MX1 ISG15 IFIT3 IFI44 IFI35 IRF7 ... #> IL2 STAT5 SIGNALING : JUNB PPP1R15A SERPINE1 ID2 IFNGR2 PMEPA1 ... #> HEDGEHOG SIGNALING : VEGFA VLDLR MYH9 ERO1A DDIT4 STC2 ... #> APICAL JUNCTION : EGFR ADAM10 CLTC AP2M1 ARF1 MAPK1 ... #> APOPTOSIS : SPTAN1 CDKN1A GSN GPX3 CLU GADD45B ... #> P53 PATHWAY : BTG2 TAP1 CDKN2B ATF3 BTG1 RRAD ...