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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
#> 1 1 sterol metabolic process
#> 2 1 sterol metabolic process
#> 3 1 sterol metabolic process
#> 4 1 sterol metabolic process
#> 5 1 sterol metabolic process
#> 6 1 sterol metabolic process
#> Term Annot_hf36_vs_hf12
#> 1 alcohol biosynthetic process GO:0046165
#> 2 alcohol metabolic process GO:0006066
#> 3 cholesterol biosynthetic process GO:0006695
#> 4 cholesterol metabolic process GO:0008203
#> 5 organic hydroxy compound biosynthetic process GO:1901617
#> 6 organic hydroxy compound metabolic process GO:1901615
#> Annotated_hf36_vs_hf12 Significant_hf36_vs_hf12 Pvalue_hf36_vs_hf12
#> 1 96 26 1.504810e-09
#> 2 242 50 4.285033e-12
#> 3 43 21 1.312468e-13
#> 4 114 37 9.677181e-16
#> 5 191 40 3.826113e-10
#> 6 410 69 1.148054e-11
#> Padj_hf36_vs_hf12
#> 1 3.482786e-08
#> 2 1.359188e-10
#> 3 4.967101e-12
#> 4 4.467717e-14
#> 5 9.477152e-09
#> 6 3.455133e-10
#> GeneID_hf36_vs_hf12
#> 1 Dhcr24,Insig1,Tm7sf2,Lep,Cyp51,Sc5d,Plek,Insig2,Sptlc2,Fgf1,Fdps,Lss,Mvd,Nsdhl,Fdft1,Hsd17b7,Srebf1,Apoe,Pmvk,Ptk2b,Hmgcr,Mvk,Hmgcs1,Isyna1,G6pdx,Scp2
#> 2 Hdlbp,Acadvl,Dhcr24,Ephx2,Insig1,Tm7sf2,Lep,Cyp51,Sc5d,Dgat2,Plcb1,Rbp4,Plek,Tpi1,Ldlr,Insig2,Sptlc2,Fgf1,Fdps,Mvd,Dhrs3,Lss,Nsdhl,Fdft1,Inpp5k,Hsd17b7,Srebf1,Acadl,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Lrp5,Ptk2b,Srebf2,Vldlr,Hmgcr,Mtmr2,Abca2,Coq2,Dhrs4,Itpkb,Mvk,Hmgcs1,Cln8,Sqle,Isyna1,G6pdx,Scp2
#> 3 Dhcr24,Insig1,Tm7sf2,Cyp51,Sc5d,Insig2,Fgf1,Fdps,Lss,Fdft1,Mvd,Hsd17b7,Srebf1,Nsdhl,Apoe,Pmvk,Hmgcr,Mvk,Hmgcs1,G6pdx,Scp2
#> 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 Per2,Snai1,Dhcr24,Insig1,Tm7sf2,Wnt5a,Lep,Nr4a2,Cyp51,Sc5d,Plek,Tph2,Stard4,Insig2,Sptlc2,Fgf1,Fdps,Lss,Mvd,Nsdhl,Fdft1,Hsd17b7,Srebf1,Ldha,Apoe,Pmvk,Ptk2b,Hmgcr,Dab2,Lbr,Cdh3,Mvk,Hmgcs1,Sqle,Isyna1,Ctns,G6pdx,Pltp,Scp2,Msmo1
#> 6 Hdlbp,Per2,Snai1,Acadvl,Dhcr24,Pnkd,Park2,Ephx2,Insig1,Cpq,Tm7sf2,Wnt5a,Lep,Nr4a2,Cyp51,Sc5d,Dgat2,Plcb1,Rbp4,Plek,Tpi1,Tph2,Stard4,Ldlr,Insig2,Sptlc2,Fgf1,Fdps,Mvd,Dhrs3,Hprt,Lss,Nsdhl,Fdft1,Inpp5k,Hsd17b7,Srebf1,Comt,Acadl,Ldha,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Lrp5,Ptk2b,Srebf2,Vldlr,Hmgcr,Mtmr2,Dab2,Lbr,Abca2,Coq2,Cdh3,Dhrs4,Itpkb,Mvk,Hmgcs1,Cln8,Sqle,Isyna1,Duoxa1,Ctns,G6pdx,Pltp,Scp2,Msmo1
#> Annot_wt36_vs_wt12 Annotated_wt36_vs_wt12 Significant_wt36_vs_wt12
#> 1 GO:0046165 96 22
#> 2 GO:0006066 242 40
#> 3 GO:0006695 43 18
#> 4 GO:0008203 114 30
#> 5 GO:1901617 191 32
#> 6 GO:1901615 410 52
#> Pvalue_wt36_vs_wt12 Padj_wt36_vs_wt12
#> 1 1.693687e-09 7.956122e-08
#> 2 2.997181e-11 1.792198e-09
#> 3 6.897061e-13 5.732140e-11
#> 4 3.831384e-14 3.863568e-12
#> 5 1.979968e-09 9.130789e-08
#> 6 8.872210e-10 4.385655e-08
#> GeneID_wt36_vs_wt12
#> 1 Dhcr24,Insig1,Tm7sf2,Lep,Cyp51,Sc5d,Gba,Sptlc2,Fdps,Mvd,Lss,Nsdhl,Fdft1,Hsd17b7,Hmgcs2,Apoe,Pmvk,Ptk2b,Hmgcr,Mvk,Hmgcs1,G6pdx
#> 2 Dhcr24,Insig1,Tm7sf2,Pon1,Lep,Cyp51,Sc5d,Dgat2,Tpi1,Gba,Ldlr,Sptlc2,Fdps,Dhrs3,Lss,Mvd,Nsdhl,Fdft1,Hsd17b7,Hmgcs2,Acadl,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Ptk2b,Srebf2,Aplp2,Hmgcr,Mtmr2,Abca2,Itpkb,Dhrs4,Mvk,Hmgcs1,Aldh1a1,Sqle,G6pdx,Slc5a3
#> 3 Dhcr24,Insig1,Tm7sf2,Cyp51,Sc5d,Fdps,Mvd,Lss,Fdft1,Nsdhl,Hsd17b7,Hmgcs2,Apoe,Pmvk,Hmgcr,Mvk,Hmgcs1,G6pdx
#> 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 Per2,Dhcr24,Insig1,Tm7sf2,Lep,Nr4a2,Cyp51,Sc5d,Gba,Tph2,Stard4,Sptlc2,Fdps,Mvd,Lss,Nsdhl,Fdft1,Hsd17b7,Hmgcs2,Ldha,Apoe,Dkk3,Pmvk,Ptk2b,Hmgcr,Cdh3,Mvk,Hmgcs1,Sqle,G6pdx,Pltp,Msmo1
#> 6 Per2,Dhcr24,Insig1,Tm7sf2,Pon1,Lep,Nr4a2,Cyp51,Sc5d,Dgat2,Tpi1,Gba,Tph2,Stard4,Ldlr,Sptlc2,Fdps,Mvd,Dhrs3,Hprt,Lss,Nsdhl,Fdft1,Hsd17b7,Hmgcs2,Comt,Acadl,Ldha,Abca1,Apoe,Mbtps1,Npc2,Dkk3,Pmvk,Ptk2b,Srebf2,Aplp2,Hmgcr,Mtmr2,Cdh3,Abca2,Dhrs4,Itpkb,Mvk,Lipa,Hmgcs1,Aldh1a1,Sqle,G6pdx,Pltp,Slc5a3,Msmo1
#> GeneID
#> 1 Dhcr24,Insig1,Tm7sf2,Lep,Cyp51,Sc5d,Plek,Insig2,Sptlc2,Fgf1,Fdps,Lss,Mvd,Nsdhl,Fdft1,Hsd17b7,Srebf1,Apoe,Pmvk,Ptk2b,Hmgcr,Mvk,Hmgcs1,Isyna1,G6pdx,Scp2,Gba,Hmgcs2
#> 2 Hdlbp,Acadvl,Dhcr24,Ephx2,Insig1,Tm7sf2,Lep,Cyp51,Sc5d,Dgat2,Plcb1,Rbp4,Plek,Tpi1,Ldlr,Insig2,Sptlc2,Fgf1,Fdps,Mvd,Dhrs3,Lss,Nsdhl,Fdft1,Inpp5k,Hsd17b7,Srebf1,Acadl,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Lrp5,Ptk2b,Srebf2,Vldlr,Hmgcr,Mtmr2,Abca2,Coq2,Dhrs4,Itpkb,Mvk,Hmgcs1,Cln8,Sqle,Isyna1,G6pdx,Scp2,Pon1,Gba,Hmgcs2,Aplp2,Aldh1a1,Slc5a3
#> 3 Dhcr24,Insig1,Tm7sf2,Cyp51,Sc5d,Insig2,Fgf1,Fdps,Lss,Fdft1,Mvd,Hsd17b7,Srebf1,Nsdhl,Apoe,Pmvk,Hmgcr,Mvk,Hmgcs1,G6pdx,Scp2,Hmgcs2
#> 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,Pon1,Hmgcs2,Aplp2
#> 5 Per2,Snai1,Dhcr24,Insig1,Tm7sf2,Wnt5a,Lep,Nr4a2,Cyp51,Sc5d,Plek,Tph2,Stard4,Insig2,Sptlc2,Fgf1,Fdps,Lss,Mvd,Nsdhl,Fdft1,Hsd17b7,Srebf1,Ldha,Apoe,Pmvk,Ptk2b,Hmgcr,Dab2,Lbr,Cdh3,Mvk,Hmgcs1,Sqle,Isyna1,Ctns,G6pdx,Pltp,Scp2,Msmo1,Gba,Hmgcs2,Dkk3
#> 6 Hdlbp,Per2,Snai1,Acadvl,Dhcr24,Pnkd,Park2,Ephx2,Insig1,Cpq,Tm7sf2,Wnt5a,Lep,Nr4a2,Cyp51,Sc5d,Dgat2,Plcb1,Rbp4,Plek,Tpi1,Tph2,Stard4,Ldlr,Insig2,Sptlc2,Fgf1,Fdps,Mvd,Dhrs3,Hprt,Lss,Nsdhl,Fdft1,Inpp5k,Hsd17b7,Srebf1,Comt,Acadl,Ldha,Abca1,Apoe,Mbtps1,Npc2,Pmvk,Lrp5,Ptk2b,Srebf2,Vldlr,Hmgcr,Mtmr2,Dab2,Lbr,Abca2,Coq2,Cdh3,Dhrs4,Itpkb,Mvk,Hmgcs1,Cln8,Sqle,Isyna1,Duoxa1,Ctns,G6pdx,Pltp,Scp2,Msmo1,Pon1,Gba,Hmgcs2,Dkk3,Aplp2,Lipa,Aldh1a1,Slc5a3
#> Pvalue Padj DatasetCount
#> 1 1.599249e-09 5.719454e-08 2
#> 2 1.712842e-11 9.640583e-10 2
#> 3 4.104765e-13 3.114425e-11 2
#> 4 1.964078e-14 1.954122e-12 2
#> 5 1.181289e-09 5.039252e-08 2
#> 6 4.493508e-10 2.210103e-08 2These 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.
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