Author: Sarah Hong
Date: 2025-12-13

# Workflow: richCluster Example

#### Sarah Hong

#### 2025-12-13

## Load or Generate Clustering Data

    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-Level Visualizations

    c_hmap <- cluster_hmap(cluster_result)
    #> Warning in fix_not_all_unique(rownames(x)): Not all the values are unique -
    #> manually added prefix numbers
    c_hmap

    c_bar <- cluster_bar(cluster_result)
    c_bar
    #> Warning: Ignoring 3 observations

    c_dot <- cluster_dot(cluster_result)
    c_dot
    #> Warning: Ignoring 3 observations
    #> Warning: `line.width` does not currently support multiple values.
    #> Warning: `line.width` does not currently support multiple values.

## Term-Level Visualizations

    clusters <- c("blood vessel development", "response to lipoprotein particle", "positive regulation of cell death")
    terms <- c("myelination", "lipid oxidation")

    t_hmap <- term_hmap(cluster_result, clusters, terms, value_type = "Padj")
    t_hmap

    t_bar <- term_bar(cluster_result, 1)
    t_bar

    t_dot <- term_dot(cluster_result, 1)
    t_dot
    #> Warning: `line.width` does not currently support multiple values.
    #> Warning: `line.width` does not currently support multiple values.

## Export Results

    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-13