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load_cluster_data <- function(from_scratch=FALSE) {
if (!from_scratch) {
cluster_result <- readRDS(system.file("extdata", "cluster_result.rds", package = "richCluster"))
} else {
rr1 <- read.delim(system.file("extdata", "HF36wk_vs_HF12wk.txt", package="richCluster"))
rr2 <- read.delim(system.file("extdata", "HF36wk_vs_WT12wk.txt", package="richCluster"))
enrichment_results <- list(rr1, rr2)
rr_names <- c('hf36_vs_hf12', 'wt36_vs_wt12')
cluster_result <- richCluster::cluster(
enrichment_results, df_names = rr_names, min_terms = 3, min_value=0.0001,
distance_metric = "kappa", distance_cutoff = 0.5,
linkage_method = "average", linkage_cutoff = 0.5
)
}
return(cluster_result)
}
cluster_result <- load_cluster_data(from_scratch = FALSE)cluster_df <- export_df(cluster_result)
head(cluster_df)
#> Cluster ClusterName Term
#> 1 1 blood vessel development blood vessel development
#> 2 1 blood vessel development cardiovascular system development
#> 3 1 blood vessel development vasculature development
#> 4 2 sterol metabolic process cholesterol metabolic process
#> 5 2 sterol metabolic process secondary alcohol metabolic process
#> 6 2 sterol metabolic process sterol metabolic process
#> Annot_hf36_vs_hf12 Annotated_hf36_vs_hf12 Significant_hf36_vs_hf12
#> 1 GO:0001568 634 106
#> 2 GO:0072358 677 109
#> 3 GO:0001944 663 109
#> 4 GO:0008203 114 37
#> 5 GO:1902652 118 37
#> 6 GO:0016125 124 39
#> Pvalue_hf36_vs_hf12 Padj_hf36_vs_hf12
#> 1 4.878788e-17 2.655627e-15
#> 2 2.716755e-16 1.345862e-14
#> 3 5.960167e-17 3.166069e-15
#> 4 9.677181e-16 4.467717e-14
#> 5 3.381284e-15 1.490808e-13
#> 6 5.421669e-16 2.542993e-14
#> GeneID_hf36_vs_hf12
#> 1 Slit2,Ctgf,Tcf7l2,Anxa2,Mmp19,Col1a2,Fap,Nr4a1,Jak1,Pdgfa,Angptl4,Spi1,Mfge8,Wnt5a,Lep,Pde2a,Arhgap24,C3ar1,Aldh1a2,Tgfa,Pdgfrb,Rgcc,Lox,Itgb1bp1,C6,Pf4,Enpep,Thy1,Lrg1,Stab1,Acvr2b,Tnfaip2,Ecscr,Ccl11,Serpine1,Fzd5,Parva,Syk,Cd36,Adam8,Bmper,Tnfrsf1a,Ndst1,Jun,Fgf1,Shh,Ccm2,Arid2,Nsdhl,Ephb2,Gpi1,Cd34,Itgb2,Gpld1,Xbp1,Cxcl12,Atp5b,Cela1,Emp2,Ntrk2,Ddah1,Anpep,Adam15,Apoe,Runx1,Hpgd,Pik3cb,Col8a2,Sparc,C5ar1,Gpc3,Ptger4,Hif3a,Vav3,Tbxa2r,Thbs1,Lrp5,Bmp7,Ptk2b,Hspb1,Jam3,Gpx1,Notch2,Cybb,Ccl2,Ccr2,Serpinf1,Lgals3,Myh9,Egln1,Pik3r6,Ppp1r16b,Mmp9,Qk,Srpx2,Ncoa6,Sema5a,Itgav,Htatip2,Cib1,Sema4a,Ctsh,Hdac9,Cdh2,Enpp2,Rapgef3
#> 2 Slit2,Ctgf,Tcf7l2,Anxa2,Mmp19,Col1a2,Fap,Nr4a1,Jak1,Pdgfa,Angptl4,Spi1,Mfge8,Wnt5a,Lep,Pde2a,Arhgap24,C3ar1,Aldh1a2,Tgfa,Pdgfrb,Rgcc,Lox,Sgcb,Itgb1bp1,C6,Pf4,Enpep,Thy1,Lrg1,Stab1,Acvr2b,Tnfaip2,Ecscr,Ccl11,Serpine1,Fzd5,Parva,Syk,Cd36,Adam8,Bmper,Tnfrsf1a,Ndst1,Jun,Fgf1,Shh,Ccm2,Arid2,Nsdhl,Ephb2,Gpi1,Cd34,Itgb2,Gpld1,Xbp1,Cxcl12,Atp5b,Cela1,Emp2,Ntrk2,Prox2,Ddah1,Anpep,Adam15,Apoe,Runx1,Hpgd,Pik3cb,Col8a2,Sparc,C5ar1,Gpc3,Ptger4,Hif3a,Vav3,Tbxa2r,Thbs1,Lrp5,Bmp7,Ptk2b,Hspb1,Jam3,Gpx1,Notch2,Cybb,Ccl2,Ccr2,Serpinf1,Lgals3,Myh9,Egln1,Pik3r6,Ppp1r16b,Mmp9,Qk,Igf1,Srpx2,Ncoa6,Sema5a,Itgav,Htatip2,Cib1,Sema4a,Ctsh,Hdac9,Cdh2,Enpp2,Rapgef3
#> 3 Slit2,Ctgf,Tcf7l2,Anxa2,Mmp19,Col1a2,Fap,Nr4a1,Jak1,Pdgfa,Angptl4,Spi1,Mfge8,Wnt5a,Lep,Pde2a,Arhgap24,C3ar1,Aldh1a2,Tgfa,Pdgfrb,Rgcc,Lox,Sgcb,Itgb1bp1,C6,Pf4,Enpep,Thy1,Lrg1,Stab1,Acvr2b,Tnfaip2,Ecscr,Ccl11,Serpine1,Fzd5,Parva,Syk,Cd36,Adam8,Bmper,Tnfrsf1a,Ndst1,Jun,Fgf1,Shh,Ccm2,Arid2,Nsdhl,Ephb2,Gpi1,Cd34,Itgb2,Gpld1,Xbp1,Cxcl12,Atp5b,Cela1,Emp2,Ntrk2,Prox2,Ddah1,Anpep,Adam15,Apoe,Runx1,Hpgd,Pik3cb,Col8a2,Sparc,C5ar1,Gpc3,Ptger4,Hif3a,Vav3,Tbxa2r,Thbs1,Lrp5,Bmp7,Ptk2b,Hspb1,Jam3,Gpx1,Notch2,Cybb,Ccl2,Ccr2,Serpinf1,Lgals3,Myh9,Egln1,Pik3r6,Ppp1r16b,Mmp9,Qk,Igf1,Srpx2,Ncoa6,Sema5a,Itgav,Htatip2,Cib1,Sema4a,Ctsh,Hdac9,Cdh2,Enpp2,Rapgef3
#> 4 Hdlbp,Acadvl,Dhcr24,Ephx2,Insig1,Tm7sf2,Lep,Cyp51,Sc5d,Dgat2,Ldlr,Insig2,Fgf1,Fdps,Mvd,Lss,Nsdhl,Fdft1,Hsd17b7,Srebf1,Acadl,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Lrp5,Srebf2,Vldlr,Hmgcr,Abca2,Mvk,Hmgcs1,Cln8,Sqle,G6pdx,Scp2
#> 5 Hdlbp,Acadvl,Dhcr24,Ephx2,Insig1,Tm7sf2,Lep,Cyp51,Sc5d,Dgat2,Ldlr,Insig2,Fgf1,Fdps,Mvd,Lss,Nsdhl,Fdft1,Hsd17b7,Srebf1,Acadl,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Lrp5,Srebf2,Vldlr,Hmgcr,Abca2,Mvk,Hmgcs1,Cln8,Sqle,G6pdx,Scp2
#> 6 Hdlbp,Acadvl,Dhcr24,Ephx2,Insig1,Tm7sf2,Lep,Cyp51,Sc5d,Dgat2,Ldlr,Insig2,Fgf1,Fdps,Mvd,Lss,Nsdhl,Fdft1,Hsd17b7,Srebf1,Acadl,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Lrp5,Srebf2,Vldlr,Hmgcr,Lbr,Abca2,Mvk,Hmgcs1,Cln8,Sqle,G6pdx,Scp2,Msmo1
#> Annot_wt36_vs_wt12 Annotated_wt36_vs_wt12 Significant_wt36_vs_wt12
#> 1 GO:0001568 634 67
#> 2 GO:0072358 677 70
#> 3 GO:0001944 663 69
#> 4 GO:0008203 114 30
#> 5 GO:1902652 118 30
#> 6 GO:0016125 124 32
#> Pvalue_wt36_vs_wt12 Padj_wt36_vs_wt12
#> 1 8.139403e-09 3.156836e-07
#> 2 9.222440e-09 3.504990e-07
#> 3 9.065615e-09 3.462790e-07
#> 4 3.831384e-14 3.863568e-12
#> 5 1.038092e-13 9.813860e-12
#> 6 9.917374e-15 1.136441e-12
#> GeneID_wt36_vs_wt12
#> 1 Slit2,Ctgf,Tcf7l2,Anxa2,Col1a2,Nr4a1,Pdgfa,Angptl4,Mfge8,Lep,Pde2a,Arhgap24,C3ar1,Pdgfrb,Lox,Plxdc1,C6,Pf4,Thy1,Col1a1,Serpine1,Ddit3,Pknox1,Syk,Cd36,Adam8,Ndst1,Jun,Nsdhl,Itgb2,Ccl5,Xbp1,Cxcl12,Cela1,Emp2,Ntrk2,Ddah1,Ephb3,Btg1,Apoe,Hpgd,Pik3cb,Sparc,C5ar1,Hif3a,Smo,Vav3,Plxnd1,Ptk2b,Hspb1,Notch2,Gpx1,Cybb,Ets1,Ccr2,Lgals3,Setd2,Vezf1,Adm,Reck,Ppp1r16b,Qk,Srpx2,Sema5a,Htatip2,Unc5b,Hdac9
#> 2 Slit2,Ctgf,Tcf7l2,Anxa2,Col1a2,Nr4a1,Pdgfa,Angptl4,Mfge8,Lep,Pde2a,Arhgap24,C3ar1,Pdgfrb,Lox,Plxdc1,C6,Pf4,Thy1,Col1a1,Serpine1,Ddit3,Pknox1,Syk,Cd36,Adam8,Ndst1,Jun,Nxn,Nsdhl,Itgb2,Ccl5,Xbp1,Cxcl12,Cela1,Emp2,Ntrk2,Prox2,Ddah1,Ephb3,Btg1,Apoe,Hpgd,Pik3cb,Sparc,C5ar1,Hif3a,Smo,Errfi1,Vav3,Plxnd1,Ptk2b,Hspb1,Notch2,Gpx1,Cybb,Ets1,Ccr2,Lgals3,Setd2,Vezf1,Adm,Reck,Ppp1r16b,Qk,Srpx2,Sema5a,Htatip2,Unc5b,Hdac9
#> 3 Slit2,Ctgf,Tcf7l2,Anxa2,Col1a2,Nr4a1,Pdgfa,Angptl4,Mfge8,Lep,Pde2a,Arhgap24,C3ar1,Pdgfrb,Lox,Plxdc1,C6,Pf4,Thy1,Col1a1,Serpine1,Ddit3,Pknox1,Syk,Cd36,Adam8,Ndst1,Jun,Nsdhl,Itgb2,Ccl5,Xbp1,Cxcl12,Cela1,Emp2,Ntrk2,Prox2,Ddah1,Ephb3,Btg1,Apoe,Hpgd,Pik3cb,Sparc,C5ar1,Hif3a,Smo,Errfi1,Vav3,Plxnd1,Ptk2b,Hspb1,Notch2,Gpx1,Cybb,Ets1,Ccr2,Lgals3,Setd2,Vezf1,Adm,Reck,Ppp1r16b,Qk,Srpx2,Sema5a,Htatip2,Unc5b,Hdac9
#> 4 Dhcr24,Insig1,Tm7sf2,Pon1,Lep,Cyp51,Sc5d,Dgat2,Ldlr,Fdps,Mvd,Lss,Nsdhl,Fdft1,Hsd17b7,Hmgcs2,Acadl,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Srebf2,Aplp2,Hmgcr,Abca2,Mvk,Hmgcs1,Sqle,G6pdx
#> 5 Dhcr24,Insig1,Tm7sf2,Pon1,Lep,Cyp51,Sc5d,Dgat2,Ldlr,Fdps,Mvd,Lss,Nsdhl,Fdft1,Hsd17b7,Hmgcs2,Acadl,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Srebf2,Aplp2,Hmgcr,Abca2,Mvk,Hmgcs1,Sqle,G6pdx
#> 6 Dhcr24,Insig1,Tm7sf2,Pon1,Lep,Cyp51,Sc5d,Dgat2,Ldlr,Fdps,Mvd,Lss,Nsdhl,Fdft1,Hsd17b7,Hmgcs2,Acadl,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Srebf2,Aplp2,Hmgcr,Abca2,Mvk,Lipa,Hmgcs1,Sqle,G6pdx,Msmo1
#> GeneID
#> 1 Slit2,Ctgf,Tcf7l2,Anxa2,Mmp19,Col1a2,Fap,Nr4a1,Jak1,Pdgfa,Angptl4,Spi1,Mfge8,Wnt5a,Lep,Pde2a,Arhgap24,C3ar1,Aldh1a2,Tgfa,Pdgfrb,Rgcc,Lox,Itgb1bp1,C6,Pf4,Enpep,Thy1,Lrg1,Stab1,Acvr2b,Tnfaip2,Ecscr,Ccl11,Serpine1,Fzd5,Parva,Syk,Cd36,Adam8,Bmper,Tnfrsf1a,Ndst1,Jun,Fgf1,Shh,Ccm2,Arid2,Nsdhl,Ephb2,Gpi1,Cd34,Itgb2,Gpld1,Xbp1,Cxcl12,Atp5b,Cela1,Emp2,Ntrk2,Ddah1,Anpep,Adam15,Apoe,Runx1,Hpgd,Pik3cb,Col8a2,Sparc,C5ar1,Gpc3,Ptger4,Hif3a,Vav3,Tbxa2r,Thbs1,Lrp5,Bmp7,Ptk2b,Hspb1,Jam3,Gpx1,Notch2,Cybb,Ccl2,Ccr2,Serpinf1,Lgals3,Myh9,Egln1,Pik3r6,Ppp1r16b,Mmp9,Qk,Srpx2,Ncoa6,Sema5a,Itgav,Htatip2,Cib1,Sema4a,Ctsh,Hdac9,Cdh2,Enpp2,Rapgef3,Slit2,Ctgf,Tcf7l2,Anxa2,Col1a2,Nr4a1,Pdgfa,Angptl4,Mfge8,Lep,Pde2a,Arhgap24,C3ar1,Pdgfrb,Lox,Plxdc1,C6,Pf4,Thy1,Col1a1,Serpine1,Ddit3,Pknox1,Syk,Cd36,Adam8,Ndst1,Jun,Nsdhl,Itgb2,Ccl5,Xbp1,Cxcl12,Cela1,Emp2,Ntrk2,Ddah1,Ephb3,Btg1,Apoe,Hpgd,Pik3cb,Sparc,C5ar1,Hif3a,Smo,Vav3,Plxnd1,Ptk2b,Hspb1,Notch2,Gpx1,Cybb,Ets1,Ccr2,Lgals3,Setd2,Vezf1,Adm,Reck,Ppp1r16b,Qk,Srpx2,Sema5a,Htatip2,Unc5b,Hdac9
#> 2 Slit2,Ctgf,Tcf7l2,Anxa2,Mmp19,Col1a2,Fap,Nr4a1,Jak1,Pdgfa,Angptl4,Spi1,Mfge8,Wnt5a,Lep,Pde2a,Arhgap24,C3ar1,Aldh1a2,Tgfa,Pdgfrb,Rgcc,Lox,Sgcb,Itgb1bp1,C6,Pf4,Enpep,Thy1,Lrg1,Stab1,Acvr2b,Tnfaip2,Ecscr,Ccl11,Serpine1,Fzd5,Parva,Syk,Cd36,Adam8,Bmper,Tnfrsf1a,Ndst1,Jun,Fgf1,Shh,Ccm2,Arid2,Nsdhl,Ephb2,Gpi1,Cd34,Itgb2,Gpld1,Xbp1,Cxcl12,Atp5b,Cela1,Emp2,Ntrk2,Prox2,Ddah1,Anpep,Adam15,Apoe,Runx1,Hpgd,Pik3cb,Col8a2,Sparc,C5ar1,Gpc3,Ptger4,Hif3a,Vav3,Tbxa2r,Thbs1,Lrp5,Bmp7,Ptk2b,Hspb1,Jam3,Gpx1,Notch2,Cybb,Ccl2,Ccr2,Serpinf1,Lgals3,Myh9,Egln1,Pik3r6,Ppp1r16b,Mmp9,Qk,Igf1,Srpx2,Ncoa6,Sema5a,Itgav,Htatip2,Cib1,Sema4a,Ctsh,Hdac9,Cdh2,Enpp2,Rapgef3,Slit2,Ctgf,Tcf7l2,Anxa2,Col1a2,Nr4a1,Pdgfa,Angptl4,Mfge8,Lep,Pde2a,Arhgap24,C3ar1,Pdgfrb,Lox,Plxdc1,C6,Pf4,Thy1,Col1a1,Serpine1,Ddit3,Pknox1,Syk,Cd36,Adam8,Ndst1,Jun,Nxn,Nsdhl,Itgb2,Ccl5,Xbp1,Cxcl12,Cela1,Emp2,Ntrk2,Prox2,Ddah1,Ephb3,Btg1,Apoe,Hpgd,Pik3cb,Sparc,C5ar1,Hif3a,Smo,Errfi1,Vav3,Plxnd1,Ptk2b,Hspb1,Notch2,Gpx1,Cybb,Ets1,Ccr2,Lgals3,Setd2,Vezf1,Adm,Reck,Ppp1r16b,Qk,Srpx2,Sema5a,Htatip2,Unc5b,Hdac9
#> 3 Slit2,Ctgf,Tcf7l2,Anxa2,Mmp19,Col1a2,Fap,Nr4a1,Jak1,Pdgfa,Angptl4,Spi1,Mfge8,Wnt5a,Lep,Pde2a,Arhgap24,C3ar1,Aldh1a2,Tgfa,Pdgfrb,Rgcc,Lox,Sgcb,Itgb1bp1,C6,Pf4,Enpep,Thy1,Lrg1,Stab1,Acvr2b,Tnfaip2,Ecscr,Ccl11,Serpine1,Fzd5,Parva,Syk,Cd36,Adam8,Bmper,Tnfrsf1a,Ndst1,Jun,Fgf1,Shh,Ccm2,Arid2,Nsdhl,Ephb2,Gpi1,Cd34,Itgb2,Gpld1,Xbp1,Cxcl12,Atp5b,Cela1,Emp2,Ntrk2,Prox2,Ddah1,Anpep,Adam15,Apoe,Runx1,Hpgd,Pik3cb,Col8a2,Sparc,C5ar1,Gpc3,Ptger4,Hif3a,Vav3,Tbxa2r,Thbs1,Lrp5,Bmp7,Ptk2b,Hspb1,Jam3,Gpx1,Notch2,Cybb,Ccl2,Ccr2,Serpinf1,Lgals3,Myh9,Egln1,Pik3r6,Ppp1r16b,Mmp9,Qk,Igf1,Srpx2,Ncoa6,Sema5a,Itgav,Htatip2,Cib1,Sema4a,Ctsh,Hdac9,Cdh2,Enpp2,Rapgef3,Slit2,Ctgf,Tcf7l2,Anxa2,Col1a2,Nr4a1,Pdgfa,Angptl4,Mfge8,Lep,Pde2a,Arhgap24,C3ar1,Pdgfrb,Lox,Plxdc1,C6,Pf4,Thy1,Col1a1,Serpine1,Ddit3,Pknox1,Syk,Cd36,Adam8,Ndst1,Jun,Nsdhl,Itgb2,Ccl5,Xbp1,Cxcl12,Cela1,Emp2,Ntrk2,Prox2,Ddah1,Ephb3,Btg1,Apoe,Hpgd,Pik3cb,Sparc,C5ar1,Hif3a,Smo,Errfi1,Vav3,Plxnd1,Ptk2b,Hspb1,Notch2,Gpx1,Cybb,Ets1,Ccr2,Lgals3,Setd2,Vezf1,Adm,Reck,Ppp1r16b,Qk,Srpx2,Sema5a,Htatip2,Unc5b,Hdac9
#> 4 Hdlbp,Acadvl,Dhcr24,Ephx2,Insig1,Tm7sf2,Lep,Cyp51,Sc5d,Dgat2,Ldlr,Insig2,Fgf1,Fdps,Mvd,Lss,Nsdhl,Fdft1,Hsd17b7,Srebf1,Acadl,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Lrp5,Srebf2,Vldlr,Hmgcr,Abca2,Mvk,Hmgcs1,Cln8,Sqle,G6pdx,Scp2,Dhcr24,Insig1,Tm7sf2,Pon1,Lep,Cyp51,Sc5d,Dgat2,Ldlr,Fdps,Mvd,Lss,Nsdhl,Fdft1,Hsd17b7,Hmgcs2,Acadl,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Srebf2,Aplp2,Hmgcr,Abca2,Mvk,Hmgcs1,Sqle,G6pdx
#> 5 Hdlbp,Acadvl,Dhcr24,Ephx2,Insig1,Tm7sf2,Lep,Cyp51,Sc5d,Dgat2,Ldlr,Insig2,Fgf1,Fdps,Mvd,Lss,Nsdhl,Fdft1,Hsd17b7,Srebf1,Acadl,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Lrp5,Srebf2,Vldlr,Hmgcr,Abca2,Mvk,Hmgcs1,Cln8,Sqle,G6pdx,Scp2,Dhcr24,Insig1,Tm7sf2,Pon1,Lep,Cyp51,Sc5d,Dgat2,Ldlr,Fdps,Mvd,Lss,Nsdhl,Fdft1,Hsd17b7,Hmgcs2,Acadl,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Srebf2,Aplp2,Hmgcr,Abca2,Mvk,Hmgcs1,Sqle,G6pdx
#> 6 Hdlbp,Acadvl,Dhcr24,Ephx2,Insig1,Tm7sf2,Lep,Cyp51,Sc5d,Dgat2,Ldlr,Insig2,Fgf1,Fdps,Mvd,Lss,Nsdhl,Fdft1,Hsd17b7,Srebf1,Acadl,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Lrp5,Srebf2,Vldlr,Hmgcr,Lbr,Abca2,Mvk,Hmgcs1,Cln8,Sqle,G6pdx,Scp2,Msmo1,Dhcr24,Insig1,Tm7sf2,Pon1,Lep,Cyp51,Sc5d,Dgat2,Ldlr,Fdps,Mvd,Lss,Nsdhl,Fdft1,Hsd17b7,Hmgcs2,Acadl,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Srebf2,Aplp2,Hmgcr,Abca2,Mvk,Lipa,Hmgcs1,Sqle,G6pdx,Msmo1
#> Pvalue Padj
#> 1 4.069702e-09 1.578418e-07
#> 2 4.611220e-09 1.752495e-07
#> 3 4.532808e-09 1.731395e-07
#> 4 1.964078e-14 1.954122e-12
#> 5 5.359523e-14 4.981471e-12
#> 6 5.229770e-15 5.809354e-13These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.