Perform a k-fold cross-validation using the function bn.cv to estimate the entropy loss. For details and examples regarding the statistical assesment of an inferred model, we refer to the Vignette Section 7.
A reconstructed model (the output of tronco.capri or tronco.caprese)
The names of the selected regularizers (bic, aic or caprese)
a positive integer number, the number of times cross-validation will be run
a positive integer number, the number of groups into which the data will be split
A parameter to disable/enable verbose messages.
data(test_model)
tronco.kfold.eloss(test_model, k = 2, runs = 2)
#> Calculating entropy loss with k-fold cross-validation
#> [ k = 2 | runs = 2 | regularizer = capri_bic ] ... DONE
#> Model logLik = -235.8336
#> Mean eloss = 7.414657 | 3.144021 %
#> Stdev eloss = 0.04683479
#> Calculating entropy loss with k-fold cross-validation
#> [ k = 2 | runs = 2 | regularizer = capri_aic ] ... DONE
#> Model logLik = -224.5718
#> Mean eloss = 6.973349 | 3.105176 %
#> Stdev eloss = 0.1433313
#> $genotypes
#> gene 4 gene 5 gene 7 gene 29 gene 30 gene 31 gene 32 gene 33 gene 34
#> patient 1 0 0 0 1 0 0 0 0 0
#> patient 2 0 0 0 1 0 0 0 0 1
#> patient 3 0 0 0 1 1 0 0 0 0
#> patient 4 0 0 0 1 0 0 0 0 1
#> patient 5 0 0 0 1 0 0 0 0 0
#> patient 6 0 0 0 1 0 0 0 0 0
#> patient 7 0 0 0 1 0 0 0 0 0
#> patient 8 0 0 0 1 0 0 0 0 0
#> patient 9 0 0 1 1 0 0 0 0 0
#> patient 10 0 0 0 1 0 0 0 0 0
#> patient 11 0 0 0 1 0 0 0 0 0
#> patient 12 0 0 0 1 1 0 0 0 0
#> patient 13 0 0 0 1 0 0 0 0 0
#> patient 14 0 0 0 1 0 0 0 0 0
#> patient 15 0 0 0 0 0 0 0 0 0
#> patient 16 0 0 0 0 0 0 0 0 0
#> patient 17 0 0 0 0 1 0 0 1 0
#> patient 18 0 0 0 0 0 0 0 0 0
#> patient 19 0 0 0 0 0 0 0 0 0
#> patient 20 0 0 0 0 0 0 0 1 0
#> patient 21 0 0 1 0 0 0 1 0 0
#> patient 22 0 0 0 0 0 0 0 0 0
#> patient 23 1 0 0 0 0 0 0 1 0
#> patient 24 1 0 1 0 0 0 0 1 1
#> patient 25 1 0 0 0 0 0 0 0 0
#> patient 26 0 0 0 0 0 0 0 0 0
#> patient 27 0 1 1 0 0 0 1 0 0
#> patient 28 0 0 0 0 0 0 0 0 0
#> patient 29 0 0 1 0 0 0 0 1 0
#> patient 30 0 0 0 0 0 0 0 0 0
#> patient 31 0 0 0 0 0 0 0 0 0
#> patient 32 0 0 1 0 0 1 0 0 0
#> patient 33 0 0 0 0 0 0 0 0 0
#> patient 34 0 0 0 0 0 0 1 0 0
#> patient 35 0 0 0 0 0 0 0 0 0
#> patient 36 0 0 0 0 0 0 0 0 0
#> patient 37 0 0 0 0 0 0 0 0 0
#> patient 38 0 0 0 0 0 0 0 1 0
#> patient 39 0 0 1 0 0 0 0 0 0
#> patient 40 0 0 0 0 0 0 0 0 0
#> gene 36 gene 40 gene 44 gene 47 gene 49 gene 50 gene 51 gene 52
#> patient 1 0 0 0 0 0 0 0 0
#> patient 2 0 0 0 0 0 0 0 0
#> patient 3 0 0 0 0 0 0 0 0
#> patient 4 0 0 0 0 0 0 0 0
#> patient 5 0 0 0 0 0 0 0 0
#> patient 6 0 0 0 0 0 0 0 0
#> patient 7 0 0 0 0 0 1 0 0
#> patient 8 0 0 0 0 0 0 0 0
#> patient 9 0 0 0 0 0 0 0 0
#> patient 10 0 0 0 0 0 0 0 0
#> patient 11 0 0 0 0 0 0 0 0
#> patient 12 0 0 1 0 0 0 0 0
#> patient 13 0 0 0 0 0 0 0 0
#> patient 14 0 0 0 0 0 0 0 0
#> patient 15 1 0 0 0 0 0 0 0
#> patient 16 0 0 0 0 0 0 0 0
#> patient 17 0 0 0 0 0 0 0 0
#> patient 18 0 0 0 0 0 0 0 0
#> patient 19 0 0 0 0 0 0 0 1
#> patient 20 0 0 0 0 0 0 1 0
#> patient 21 0 0 0 0 0 0 0 0
#> patient 22 0 1 0 0 0 0 0 0
#> patient 23 0 0 0 0 0 0 0 0
#> patient 24 0 0 0 0 0 0 0 0
#> patient 25 0 0 0 0 0 0 0 0
#> patient 26 0 0 0 0 0 0 0 0
#> patient 27 0 0 0 0 0 0 0 0
#> patient 28 0 0 0 0 0 0 0 0
#> patient 29 0 0 0 0 0 0 0 0
#> patient 30 0 0 0 0 0 0 0 0
#> patient 31 0 0 0 1 0 0 0 0
#> patient 32 0 0 0 0 0 0 0 0
#> patient 33 0 0 0 0 0 0 0 0
#> patient 34 0 0 0 0 0 0 0 0
#> patient 35 0 0 0 0 0 0 0 0
#> patient 36 0 0 0 0 0 0 0 0
#> patient 37 0 0 0 0 0 0 0 0
#> patient 38 0 0 0 0 1 0 0 0
#> patient 39 0 0 0 0 0 0 0 0
#> patient 40 0 0 0 0 0 0 0 0
#> gene 53 gene 54 gene 55 gene 56 gene 66 gene 69 gene 77 gene 88
#> patient 1 0 0 0 0 0 0 0 0
#> patient 2 0 0 0 0 0 0 0 0
#> patient 3 0 0 0 0 0 0 0 0
#> patient 4 0 0 0 0 0 0 0 0
#> patient 5 0 0 1 0 0 0 0 0
#> patient 6 0 0 0 0 0 0 0 0
#> patient 7 0 0 0 0 0 0 0 0
#> patient 8 0 0 0 0 0 0 0 0
#> patient 9 0 0 0 0 0 0 0 0
#> patient 10 0 0 0 0 0 0 0 0
#> patient 11 0 0 0 0 0 0 0 0
#> patient 12 0 0 0 0 0 0 0 1
#> patient 13 0 0 1 0 0 0 0 1
#> patient 14 0 0 0 0 0 0 0 0
#> patient 15 0 0 0 0 0 0 0 0
#> patient 16 0 1 0 0 0 0 0 0
#> patient 17 1 0 0 0 0 0 0 0
#> patient 18 0 0 0 0 0 0 0 0
#> patient 19 0 0 0 0 0 0 0 0
#> patient 20 0 0 0 0 0 0 0 0
#> patient 21 0 0 0 0 0 0 0 0
#> patient 22 0 0 0 0 0 0 0 0
#> patient 23 0 0 0 1 0 0 0 0
#> patient 24 0 0 0 0 0 0 0 0
#> patient 25 0 0 0 1 0 1 0 0
#> patient 26 0 0 0 0 0 0 0 1
#> patient 27 0 0 0 0 0 0 0 0
#> patient 28 0 0 0 0 0 0 0 0
#> patient 29 0 0 0 0 0 0 0 1
#> patient 30 0 0 1 0 0 0 0 0
#> patient 31 0 0 0 0 0 0 1 0
#> patient 32 0 0 0 0 0 0 0 0
#> patient 33 0 0 0 0 0 0 0 0
#> patient 34 0 0 1 0 1 0 1 0
#> patient 35 0 0 0 0 0 0 0 0
#> patient 36 0 0 0 0 0 0 0 0
#> patient 37 0 0 0 0 0 0 0 0
#> patient 38 0 0 0 0 0 0 0 0
#> patient 39 0 0 0 0 0 0 0 0
#> patient 40 0 0 0 0 0 0 0 1
#> gene 89 gene 91 gene 111 XOR_EZH2 OR_CSF3R
#> patient 1 0 0 0 0 0
#> patient 2 0 1 0 0 0
#> patient 3 0 0 0 0 0
#> patient 4 0 1 0 0 0
#> patient 5 0 0 1 0 1
#> patient 6 1 0 0 1 0
#> patient 7 0 1 0 0 0
#> patient 8 0 1 0 0 0
#> patient 9 0 0 0 0 0
#> patient 10 0 0 0 0 0
#> patient 11 0 0 0 0 0
#> patient 12 0 0 0 0 0
#> patient 13 0 0 0 0 1
#> patient 14 0 0 1 0 1
#> patient 15 0 0 0 0 0
#> patient 16 0 0 0 0 0
#> patient 17 0 0 0 1 0
#> patient 18 0 0 0 0 0
#> patient 19 0 0 0 0 0
#> patient 20 0 0 0 1 0
#> patient 21 0 0 0 0 0
#> patient 22 0 0 0 0 0
#> patient 23 0 0 0 1 0
#> patient 24 0 0 0 1 0
#> patient 25 0 0 0 0 0
#> patient 26 0 0 0 0 0
#> patient 27 0 0 0 1 0
#> patient 28 0 0 0 0 0
#> patient 29 0 0 0 1 0
#> patient 30 0 0 0 0 1
#> patient 31 0 0 0 0 0
#> patient 32 0 0 0 0 0
#> patient 33 0 0 0 0 0
#> patient 34 0 0 0 0 1
#> patient 35 0 0 1 0 1
#> patient 36 0 0 0 0 0
#> patient 37 0 0 0 0 0
#> patient 38 0 0 0 1 0
#> patient 39 0 0 0 0 0
#> patient 40 0 0 0 0 0
#>
#> $annotations
#> type event
#> gene 4 "ins_del" "TET2"
#> gene 5 "ins_del" "EZH2"
#> gene 7 "ins_del" "ASXL1"
#> gene 29 "missense_point_mutations" "SETBP1"
#> gene 30 "missense_point_mutations" "NRAS_Ex2_3"
#> gene 31 "missense_point_mutations" "KRAS_Ex2_3"
#> gene 32 "missense_point_mutations" "TET2"
#> gene 33 "missense_point_mutations" "EZH2"
#> gene 34 "missense_point_mutations" "CBL_Ex_8_9"
#> gene 36 "missense_point_mutations" "IDH2_R140"
#> gene 40 "missense_point_mutations" "SF3B1_Ex_12_15"
#> gene 44 "missense_point_mutations" "JARID_2_Ex1_18"
#> gene 47 "missense_point_mutations" "EED_Ex2_12"
#> gene 49 "missense_point_mutations" "CEBPA"
#> gene 50 "missense_point_mutations" "EPHB3"
#> gene 51 "missense_point_mutations" "ETNK1"
#> gene 52 "missense_point_mutations" "GATA2"
#> gene 53 "missense_point_mutations" "IRAK4"
#> gene 54 "missense_point_mutations" "MTA2"
#> gene 55 "missense_point_mutations" "CSF3R"
#> gene 56 "missense_point_mutations" "KIT"
#> gene 66 "nonsense_ins_del" "WT1"
#> gene 69 "nonsense_ins_del" "RUNX_1"
#> gene 77 "nonsense_ins_del" "CEBPA"
#> gene 88 "nonsense_point_mutations" "TET2"
#> gene 89 "nonsense_point_mutations" "EZH2"
#> gene 91 "nonsense_point_mutations" "ASXL1"
#> gene 111 "nonsense_point_mutations" "CSF3R"
#> XOR_EZH2 "Pattern" "XOR_EZH2"
#> OR_CSF3R "Pattern" "OR_CSF3R"
#>
#> $types
#> color
#> ins_del "khaki"
#> missense_point_mutations "lightgreen"
#> nonsense_ins_del "cornflowerblue"
#> nonsense_point_mutations "firebrick1"
#> Pattern "slateblue"
#>
#> $stages
#> [1] NA
#>
#> $hypotheses
#> $hypotheses$num.hypotheses
#> [1] 2
#>
#> $hypotheses$hlist
#> cause effect
#> [1,] "XOR_EZH2" "gene 4"
#> [2,] "XOR_EZH2" "gene 7"
#> [3,] "XOR_EZH2" "gene 29"
#> [4,] "XOR_EZH2" "gene 30"
#> [5,] "XOR_EZH2" "gene 31"
#> [6,] "XOR_EZH2" "gene 32"
#> [7,] "XOR_EZH2" "gene 34"
#> [8,] "XOR_EZH2" "gene 36"
#> [9,] "XOR_EZH2" "gene 40"
#> [10,] "XOR_EZH2" "gene 44"
#> [11,] "XOR_EZH2" "gene 47"
#> [12,] "XOR_EZH2" "gene 49"
#> [13,] "XOR_EZH2" "gene 50"
#> [14,] "XOR_EZH2" "gene 51"
#> [15,] "XOR_EZH2" "gene 52"
#> [16,] "XOR_EZH2" "gene 53"
#> [17,] "XOR_EZH2" "gene 54"
#> [18,] "XOR_EZH2" "gene 55"
#> [19,] "XOR_EZH2" "gene 56"
#> [20,] "XOR_EZH2" "gene 66"
#> [21,] "XOR_EZH2" "gene 69"
#> [22,] "XOR_EZH2" "gene 77"
#> [23,] "XOR_EZH2" "gene 88"
#> [24,] "XOR_EZH2" "gene 91"
#> [25,] "XOR_EZH2" "gene 111"
#> [26,] "gene 4" "XOR_EZH2"
#> [27,] "gene 7" "XOR_EZH2"
#> [28,] "gene 29" "XOR_EZH2"
#> [29,] "gene 30" "XOR_EZH2"
#> [30,] "gene 31" "XOR_EZH2"
#> [31,] "gene 32" "XOR_EZH2"
#> [32,] "gene 34" "XOR_EZH2"
#> [33,] "gene 36" "XOR_EZH2"
#> [34,] "gene 40" "XOR_EZH2"
#> [35,] "gene 44" "XOR_EZH2"
#> [36,] "gene 47" "XOR_EZH2"
#> [37,] "gene 49" "XOR_EZH2"
#> [38,] "gene 50" "XOR_EZH2"
#> [39,] "gene 51" "XOR_EZH2"
#> [40,] "gene 52" "XOR_EZH2"
#> [41,] "gene 53" "XOR_EZH2"
#> [42,] "gene 54" "XOR_EZH2"
#> [43,] "gene 55" "XOR_EZH2"
#> [44,] "gene 56" "XOR_EZH2"
#> [45,] "gene 66" "XOR_EZH2"
#> [46,] "gene 69" "XOR_EZH2"
#> [47,] "gene 77" "XOR_EZH2"
#> [48,] "gene 88" "XOR_EZH2"
#> [49,] "gene 91" "XOR_EZH2"
#> [50,] "gene 111" "XOR_EZH2"
#> [51,] "OR_CSF3R" "gene 4"
#> [52,] "OR_CSF3R" "gene 5"
#> [53,] "OR_CSF3R" "gene 7"
#> [54,] "OR_CSF3R" "gene 29"
#> [55,] "OR_CSF3R" "gene 30"
#> [56,] "OR_CSF3R" "gene 31"
#> [57,] "OR_CSF3R" "gene 32"
#> [58,] "OR_CSF3R" "gene 33"
#> [59,] "OR_CSF3R" "gene 34"
#> [60,] "OR_CSF3R" "gene 36"
#> [61,] "OR_CSF3R" "gene 40"
#> [62,] "OR_CSF3R" "gene 44"
#> [63,] "OR_CSF3R" "gene 47"
#> [64,] "OR_CSF3R" "gene 49"
#> [65,] "OR_CSF3R" "gene 50"
#> [66,] "OR_CSF3R" "gene 51"
#> [67,] "OR_CSF3R" "gene 52"
#> [68,] "OR_CSF3R" "gene 53"
#> [69,] "OR_CSF3R" "gene 54"
#> [70,] "OR_CSF3R" "gene 56"
#> [71,] "OR_CSF3R" "gene 66"
#> [72,] "OR_CSF3R" "gene 69"
#> [73,] "OR_CSF3R" "gene 77"
#> [74,] "OR_CSF3R" "gene 88"
#> [75,] "OR_CSF3R" "gene 89"
#> [76,] "OR_CSF3R" "gene 91"
#> [77,] "gene 4" "OR_CSF3R"
#> [78,] "gene 5" "OR_CSF3R"
#> [79,] "gene 7" "OR_CSF3R"
#> [80,] "gene 29" "OR_CSF3R"
#> [81,] "gene 30" "OR_CSF3R"
#> [82,] "gene 31" "OR_CSF3R"
#> [83,] "gene 32" "OR_CSF3R"
#> [84,] "gene 33" "OR_CSF3R"
#> [85,] "gene 34" "OR_CSF3R"
#> [86,] "gene 36" "OR_CSF3R"
#> [87,] "gene 40" "OR_CSF3R"
#> [88,] "gene 44" "OR_CSF3R"
#> [89,] "gene 47" "OR_CSF3R"
#> [90,] "gene 49" "OR_CSF3R"
#> [91,] "gene 50" "OR_CSF3R"
#> [92,] "gene 51" "OR_CSF3R"
#> [93,] "gene 52" "OR_CSF3R"
#> [94,] "gene 53" "OR_CSF3R"
#> [95,] "gene 54" "OR_CSF3R"
#> [96,] "gene 56" "OR_CSF3R"
#> [97,] "gene 66" "OR_CSF3R"
#> [98,] "gene 69" "OR_CSF3R"
#> [99,] "gene 77" "OR_CSF3R"
#> [100,] "gene 88" "OR_CSF3R"
#> [101,] "gene 89" "OR_CSF3R"
#> [102,] "gene 91" "OR_CSF3R"
#>
#> $hypotheses$hstructure
#> $hypotheses$hstructure$XOR_EZH2
#> gene 5 gene 33 gene 89 XOR_gene 5_gene 33_gene 89
#> gene 5 0 0 0 1
#> gene 33 0 0 0 1
#> gene 89 0 0 0 1
#> XOR_gene 5_gene 33_gene 89 0 0 0 0
#>
#> $hypotheses$hstructure$OR_CSF3R
#> gene 55 gene 111 OR_gene 55_gene 111
#> gene 55 0 0 1
#> gene 111 0 0 1
#> OR_gene 55_gene 111 0 0 0
#>
#>
#> $hypotheses$patterns
#> $hypotheses$patterns$XOR_EZH2
#> [1] "gene 5" "gene 33" "gene 89"
#>
#> $hypotheses$patterns$OR_CSF3R
#> [1] "gene 55" "gene 111"
#>
#>
#> $hypotheses$atoms
#> $hypotheses$atoms$`gene 4`
#> NULL
#>
#> $hypotheses$atoms$`gene 5`
#> [1] "XOR_EZH2"
#>
#> $hypotheses$atoms$`gene 7`
#> NULL
#>
#> $hypotheses$atoms$`gene 29`
#> NULL
#>
#> $hypotheses$atoms$`gene 30`
#> NULL
#>
#> $hypotheses$atoms$`gene 31`
#> NULL
#>
#> $hypotheses$atoms$`gene 32`
#> NULL
#>
#> $hypotheses$atoms$`gene 33`
#> [1] "XOR_EZH2"
#>
#> $hypotheses$atoms$`gene 34`
#> NULL
#>
#> $hypotheses$atoms$`gene 36`
#> NULL
#>
#> $hypotheses$atoms$`gene 40`
#> NULL
#>
#> $hypotheses$atoms$`gene 44`
#> NULL
#>
#> $hypotheses$atoms$`gene 47`
#> NULL
#>
#> $hypotheses$atoms$`gene 49`
#> NULL
#>
#> $hypotheses$atoms$`gene 50`
#> NULL
#>
#> $hypotheses$atoms$`gene 51`
#> NULL
#>
#> $hypotheses$atoms$`gene 52`
#> NULL
#>
#> $hypotheses$atoms$`gene 53`
#> NULL
#>
#> $hypotheses$atoms$`gene 54`
#> NULL
#>
#> $hypotheses$atoms$`gene 55`
#> [1] "OR_CSF3R"
#>
#> $hypotheses$atoms$`gene 56`
#> NULL
#>
#> $hypotheses$atoms$`gene 66`
#> NULL
#>
#> $hypotheses$atoms$`gene 69`
#> NULL
#>
#> $hypotheses$atoms$`gene 77`
#> NULL
#>
#> $hypotheses$atoms$`gene 88`
#> NULL
#>
#> $hypotheses$atoms$`gene 89`
#> [1] "XOR_EZH2"
#>
#> $hypotheses$atoms$`gene 91`
#> NULL
#>
#> $hypotheses$atoms$`gene 111`
#> [1] "OR_CSF3R"
#>
#>
#> $hypotheses$pvalues
#> $hypotheses$pvalues$XOR_EZH2
#>
#> 1 1 1
#>
#> $hypotheses$pvalues$OR_CSF3R
#>
#> 0.7226721
#>
#>
#>
#> $adj.matrix.prima.facie
#> gene 4 gene 5 gene 7 gene 29 gene 30 gene 31 gene 32 gene 33 gene 34
#> gene 4 0 0 0 0 0 0 0 0 1
#> gene 5 0 0 0 0 0 0 0 0 0
#> gene 7 0 0 0 0 0 1 1 0 1
#> gene 29 0 0 0 0 1 0 0 0 1
#> gene 30 0 0 0 0 0 0 0 0 0
#> gene 31 0 0 0 0 0 0 0 0 0
#> gene 32 0 1 0 0 0 0 0 0 0
#> gene 33 1 0 0 0 1 0 0 0 1
#> gene 34 0 0 0 0 0 0 0 0 0
#> gene 36 0 0 0 0 0 0 0 0 0
#> gene 40 0 0 0 0 0 0 0 0 0
#> gene 44 0 0 0 0 0 0 0 0 0
#> gene 47 0 0 0 0 0 0 0 0 0
#> gene 49 0 0 0 0 0 0 0 0 0
#> gene 50 0 0 0 0 0 0 0 0 0
#> gene 51 0 0 0 0 0 0 0 0 0
#> gene 52 0 0 0 0 0 0 0 0 0
#> gene 53 0 0 0 0 0 0 0 0 0
#> gene 54 0 0 0 0 0 0 0 0 0
#> gene 55 0 0 0 0 0 0 1 0 0
#> gene 56 0 0 0 0 0 0 0 0 0
#> gene 66 0 0 0 0 0 0 0 0 0
#> gene 69 0 0 0 0 0 0 0 0 0
#> gene 77 0 0 0 0 0 0 0 0 0
#> gene 88 0 0 0 0 1 0 0 0 0
#> gene 89 0 0 0 0 0 0 0 0 0
#> gene 91 0 0 0 0 0 0 0 0 1
#> gene 111 0 0 0 0 0 0 0 0 0
#> XOR_EZH2 1 0 0 0 1 0 0 0 0
#> OR_CSF3R 0 0 0 0 0 0 1 0 0
#> gene 36 gene 40 gene 44 gene 47 gene 49 gene 50 gene 51 gene 52
#> gene 4 0 0 0 0 0 0 0 0
#> gene 5 0 0 0 0 0 0 0 0
#> gene 7 0 0 0 0 0 0 0 0
#> gene 29 0 0 1 0 0 1 0 0
#> gene 30 0 0 1 0 0 0 0 0
#> gene 31 0 0 0 0 0 0 0 0
#> gene 32 0 0 0 0 0 0 0 0
#> gene 33 0 0 0 0 1 0 1 0
#> gene 34 0 0 0 0 0 0 0 0
#> gene 36 0 0 0 0 0 0 0 0
#> gene 40 0 0 0 0 0 0 0 0
#> gene 44 0 0 0 0 0 0 0 0
#> gene 47 0 0 0 0 0 0 0 0
#> gene 49 0 0 0 0 0 0 0 0
#> gene 50 0 0 0 0 0 0 0 0
#> gene 51 0 0 0 0 0 0 0 0
#> gene 52 0 0 0 0 0 0 0 0
#> gene 53 0 0 0 0 0 0 0 0
#> gene 54 0 0 0 0 0 0 0 0
#> gene 55 0 0 0 0 0 0 0 0
#> gene 56 0 0 0 0 0 0 0 0
#> gene 66 0 0 0 0 0 0 0 0
#> gene 69 0 0 0 0 0 0 0 0
#> gene 77 0 0 0 1 0 0 0 0
#> gene 88 0 0 1 0 0 0 0 0
#> gene 89 0 0 0 0 0 0 0 0
#> gene 91 0 0 0 0 0 1 0 0
#> gene 111 0 0 0 0 0 0 0 0
#> XOR_EZH2 0 0 0 0 1 0 1 0
#> OR_CSF3R 0 0 0 0 0 0 0 0
#> gene 53 gene 54 gene 55 gene 56 gene 66 gene 69 gene 77 gene 88
#> gene 4 0 0 0 1 0 1 0 0
#> gene 5 0 0 0 0 0 0 0 0
#> gene 7 0 0 0 0 0 0 0 0
#> gene 29 0 0 1 0 0 0 0 1
#> gene 30 1 0 0 0 0 0 0 0
#> gene 31 0 0 0 0 0 0 0 0
#> gene 32 0 0 0 0 1 0 1 0
#> gene 33 1 0 0 1 0 0 0 0
#> gene 34 0 0 0 0 0 0 0 0
#> gene 36 0 0 0 0 0 0 0 0
#> gene 40 0 0 0 0 0 0 0 0
#> gene 44 0 0 0 0 0 0 0 0
#> gene 47 0 0 0 0 0 0 0 0
#> gene 49 0 0 0 0 0 0 0 0
#> gene 50 0 0 0 0 0 0 0 0
#> gene 51 0 0 0 0 0 0 0 0
#> gene 52 0 0 0 0 0 0 0 0
#> gene 53 0 0 0 0 0 0 0 0
#> gene 54 0 0 0 0 0 0 0 0
#> gene 55 0 0 0 0 1 0 1 0
#> gene 56 0 0 0 0 0 1 0 0
#> gene 66 0 0 0 0 0 0 0 0
#> gene 69 0 0 0 0 0 0 0 0
#> gene 77 0 0 0 0 1 0 0 0
#> gene 88 0 0 1 0 0 0 0 0
#> gene 89 0 0 0 0 0 0 0 0
#> gene 91 0 0 0 0 0 0 0 0
#> gene 111 0 0 0 0 0 0 0 0
#> XOR_EZH2 1 0 0 1 0 0 0 0
#> OR_CSF3R 0 0 0 0 1 0 1 0
#> gene 89 gene 91 gene 111 XOR_EZH2 OR_CSF3R
#> gene 4 0 0 0 0 0
#> gene 5 0 0 0 0 0
#> gene 7 0 0 0 0 0
#> gene 29 1 1 1 0 1
#> gene 30 0 0 0 0 0
#> gene 31 0 0 0 0 0
#> gene 32 0 0 0 0 0
#> gene 33 0 0 0 0 0
#> gene 34 0 0 0 0 0
#> gene 36 0 0 0 0 0
#> gene 40 0 0 0 0 0
#> gene 44 0 0 0 0 0
#> gene 47 0 0 0 0 0
#> gene 49 0 0 0 0 0
#> gene 50 0 0 0 0 0
#> gene 51 0 0 0 0 0
#> gene 52 0 0 0 0 0
#> gene 53 0 0 0 0 0
#> gene 54 0 0 0 0 0
#> gene 55 0 0 1 0 0
#> gene 56 0 0 0 0 0
#> gene 66 0 0 0 0 0
#> gene 69 0 0 0 0 0
#> gene 77 0 0 0 0 0
#> gene 88 0 0 0 0 0
#> gene 89 0 0 0 0 0
#> gene 91 0 0 0 0 0
#> gene 111 0 0 0 0 0
#> XOR_EZH2 0 0 0 0 0
#> OR_CSF3R 0 0 0 0 0
#>
#> $confidence
#> confidence
#> temporal priority numeric,900
#> probability raising numeric,900
#> hypergeometric test numeric,900
#>
#> $model
#> $model$capri_bic
#> $model$capri_bic$probabilities
#> $model$capri_bic$probabilities$probabilities.observed
#> $model$capri_bic$probabilities$probabilities.observed$marginal.probs
#> marginal probability
#> gene 4 0.07416667
#> gene 5 0.02946970
#> gene 7 0.16984848
#> gene 29 0.35257576
#> gene 30 0.07954545
#> gene 31 0.02962121
#> gene 32 0.07318182
#> gene 33 0.14984848
#> gene 34 0.07045455
#> gene 36 0.03295455
#> gene 40 0.02727273
#> gene 44 0.02916667
#> gene 47 0.02984848
#> gene 49 0.02750000
#> gene 50 0.03166667
#> gene 51 0.02954545
#> gene 52 0.03068182
#> gene 53 0.03166667
#> gene 54 0.03060606
#> gene 55 0.10598485
#> gene 56 0.05242424
#> gene 66 0.02886364
#> gene 69 0.02916667
#> gene 77 0.05113636
#> gene 88 0.12439394
#> gene 89 0.02810606
#> gene 91 0.10007576
#> gene 111 0.07856061
#> XOR_EZH2 0.19787879
#> OR_CSF3R 0.15500000
#>
#> $model$capri_bic$probabilities$probabilities.observed$joint.probs
#> gene 4 gene 5 gene 7 gene 29 gene 30 gene 31
#> gene 4 0.07348485 0.00000000 0.02272727 0.00000000 0.00000000 0.000
#> gene 5 0.00000000 0.02484848 0.02484848 0.00000000 0.00000000 0.000
#> gene 7 0.02272727 0.02484848 0.16984848 0.02439394 0.00000000 0.025
#> gene 29 0.00000000 0.00000000 0.02439394 0.35257576 0.05090909 0.000
#> gene 30 0.00000000 0.00000000 0.00000000 0.05090909 0.07909091 0.000
#> gene 31 0.00000000 0.00000000 0.02500000 0.00000000 0.00000000 0.025
#> gene 32 0.00000000 0.02484848 0.04863636 0.00000000 0.00000000 0.000
#> gene 33 0.04939394 0.00000000 0.04696970 0.00000000 0.02818182 0.000
#> gene 34 0.02272727 0.00000000 0.02272727 0.04727273 0.00000000 0.000
#> gene 36 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 40 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 44 0.00000000 0.00000000 0.00000000 0.02378788 0.02378788 0.000
#> gene 47 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 49 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 50 0.00000000 0.00000000 0.00000000 0.02742424 0.00000000 0.000
#> gene 51 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 52 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 53 0.00000000 0.00000000 0.00000000 0.00000000 0.02818182 0.000
#> gene 54 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 55 0.00000000 0.00000000 0.00000000 0.05590909 0.00000000 0.000
#> gene 56 0.05075758 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 66 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 69 0.02409091 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 77 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 88 0.00000000 0.00000000 0.02424242 0.05075758 0.02378788 0.000
#> gene 89 0.00000000 0.00000000 0.00000000 0.02318182 0.00000000 0.000
#> gene 91 0.00000000 0.00000000 0.00000000 0.10000000 0.00000000 0.000
#> gene 111 0.00000000 0.00000000 0.00000000 0.05287879 0.00000000 0.000
#> XOR_EZH2 0.04939394 0.02484848 0.07181818 0.02318182 0.02818182 0.000
#> OR_CSF3R 0.00000000 0.00000000 0.00000000 0.07984848 0.00000000 0.000
#> gene 32 gene 33 gene 34 gene 36 gene 40 gene 44
#> gene 4 0.00000000 0.04939394 0.02272727 0.00000000 0.00000000 0.00000000
#> gene 5 0.02484848 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 7 0.04863636 0.04696970 0.02272727 0.00000000 0.00000000 0.00000000
#> gene 29 0.00000000 0.00000000 0.04727273 0.00000000 0.00000000 0.02378788
#> gene 30 0.00000000 0.02818182 0.00000000 0.00000000 0.00000000 0.02378788
#> gene 31 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 32 0.07257576 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 33 0.00000000 0.14984848 0.02272727 0.00000000 0.00000000 0.00000000
#> gene 34 0.00000000 0.02272727 0.07000000 0.00000000 0.00000000 0.00000000
#> gene 36 0.00000000 0.00000000 0.00000000 0.02878788 0.00000000 0.00000000
#> gene 40 0.00000000 0.00000000 0.00000000 0.00000000 0.02212121 0.00000000
#> gene 44 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.02378788
#> gene 47 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 49 0.00000000 0.02257576 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 50 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 51 0.00000000 0.02545455 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 52 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 53 0.00000000 0.02818182 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 54 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 55 0.02393939 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 56 0.00000000 0.02666667 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 66 0.02393939 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 69 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 77 0.02393939 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 88 0.00000000 0.02424242 0.00000000 0.00000000 0.00000000 0.02378788
#> gene 89 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 91 0.00000000 0.00000000 0.04727273 0.00000000 0.00000000 0.00000000
#> gene 111 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> XOR_EZH2 0.02484848 0.14984848 0.02272727 0.00000000 0.00000000 0.00000000
#> OR_CSF3R 0.02393939 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 47 gene 49 gene 50 gene 51 gene 52 gene 53
#> gene 4 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 5 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 7 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 29 0.00000000 0.00000000 0.02742424 0.00000000 0.00000000 0.00000000
#> gene 30 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.02818182
#> gene 31 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 32 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 33 0.00000000 0.02257576 0.00000000 0.02545455 0.00000000 0.02818182
#> gene 34 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 36 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 40 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 44 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 47 0.02590909 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 49 0.00000000 0.02257576 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 50 0.00000000 0.00000000 0.02742424 0.00000000 0.00000000 0.00000000
#> gene 51 0.00000000 0.00000000 0.00000000 0.02545455 0.00000000 0.00000000
#> gene 52 0.00000000 0.00000000 0.00000000 0.00000000 0.02666667 0.00000000
#> gene 53 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.02818182
#> gene 54 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 55 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 56 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 66 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 69 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 77 0.02590909 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 88 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 89 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 91 0.00000000 0.00000000 0.02742424 0.00000000 0.00000000 0.00000000
#> gene 111 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> XOR_EZH2 0.00000000 0.02257576 0.00000000 0.02545455 0.00000000 0.02818182
#> OR_CSF3R 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 54 gene 55 gene 56 gene 66 gene 69 gene 77
#> gene 4 0.00000000 0.00000000 0.05075758 0.00000000 0.02409091 0.00000000
#> gene 5 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 7 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 29 0.00000000 0.05590909 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 30 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 31 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 32 0.00000000 0.02393939 0.00000000 0.02393939 0.00000000 0.02393939
#> gene 33 0.00000000 0.00000000 0.02666667 0.00000000 0.00000000 0.00000000
#> gene 34 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 36 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 40 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 44 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 47 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.02590909
#> gene 49 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 50 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 51 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 52 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 53 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 54 0.02575758 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 55 0.00000000 0.10590909 0.00000000 0.02393939 0.00000000 0.02393939
#> gene 56 0.00000000 0.00000000 0.05075758 0.00000000 0.02409091 0.00000000
#> gene 66 0.00000000 0.02393939 0.00000000 0.02393939 0.00000000 0.02393939
#> gene 69 0.00000000 0.00000000 0.02409091 0.00000000 0.02409091 0.00000000
#> gene 77 0.00000000 0.02393939 0.00000000 0.02393939 0.00000000 0.04984848
#> gene 88 0.00000000 0.02696970 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 89 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 91 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 111 0.00000000 0.02893939 0.00000000 0.00000000 0.00000000 0.00000000
#> XOR_EZH2 0.00000000 0.00000000 0.02666667 0.00000000 0.00000000 0.00000000
#> OR_CSF3R 0.00000000 0.10590909 0.00000000 0.02393939 0.00000000 0.02393939
#> gene 88 gene 89 gene 91 gene 111 XOR_EZH2 OR_CSF3R
#> gene 4 0.00000000 0.00000000 0.00000000 0.00000000 0.04939394 0.00000000
#> gene 5 0.00000000 0.00000000 0.00000000 0.00000000 0.02484848 0.00000000
#> gene 7 0.02424242 0.00000000 0.00000000 0.00000000 0.07181818 0.00000000
#> gene 29 0.05075758 0.02318182 0.10000000 0.05287879 0.02318182 0.07984848
#> gene 30 0.02378788 0.00000000 0.00000000 0.00000000 0.02818182 0.00000000
#> gene 31 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 32 0.00000000 0.00000000 0.00000000 0.00000000 0.02484848 0.02393939
#> gene 33 0.02424242 0.00000000 0.00000000 0.00000000 0.14984848 0.00000000
#> gene 34 0.00000000 0.00000000 0.04727273 0.00000000 0.02272727 0.00000000
#> gene 36 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 40 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 44 0.02378788 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 47 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 49 0.00000000 0.00000000 0.00000000 0.00000000 0.02257576 0.00000000
#> gene 50 0.00000000 0.00000000 0.02742424 0.00000000 0.00000000 0.00000000
#> gene 51 0.00000000 0.00000000 0.00000000 0.00000000 0.02545455 0.00000000
#> gene 52 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 53 0.00000000 0.00000000 0.00000000 0.00000000 0.02818182 0.00000000
#> gene 54 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 55 0.02696970 0.00000000 0.00000000 0.02893939 0.00000000 0.10590909
#> gene 56 0.00000000 0.00000000 0.00000000 0.00000000 0.02666667 0.00000000
#> gene 66 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.02393939
#> gene 69 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 77 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.02393939
#> gene 88 0.12439394 0.00000000 0.00000000 0.00000000 0.02424242 0.02696970
#> gene 89 0.00000000 0.02318182 0.00000000 0.00000000 0.02318182 0.00000000
#> gene 91 0.00000000 0.00000000 0.10000000 0.00000000 0.00000000 0.00000000
#> gene 111 0.00000000 0.00000000 0.00000000 0.07803030 0.00000000 0.07803030
#> XOR_EZH2 0.02424242 0.02318182 0.00000000 0.00000000 0.19787879 0.00000000
#> OR_CSF3R 0.02696970 0.00000000 0.00000000 0.07803030 0.00000000 0.15500000
#>
#> $model$capri_bic$probabilities$probabilities.observed$conditional.probs
#> conditional probability
#> gene 4 0.3296259
#> gene 5 0.3395445
#> gene 7 1
#> gene 29 1
#> gene 30 1
#> gene 31 1
#> gene 32 0.2863515
#> gene 33 1
#> gene 34 0.4723694
#> gene 36 1
#> gene 40 1
#> gene 44 0.2990476
#> gene 47 0.5066667
#> gene 49 0.1506572
#> gene 50 0.2740348
#> gene 51 0.1698686
#> gene 52 1
#> gene 53 0.3542857
#> gene 54 1
#> gene 55 1
#> gene 56 0.6843718
#> gene 66 0.4681481
#> gene 69 0.4595376
#> gene 77 1
#> gene 88 1
#> gene 89 1
#> gene 91 0.283627
#> gene 111 1
#> XOR_EZH2 1
#> OR_CSF3R 1
#>
#>
#> $model$capri_bic$probabilities$probabilities.fit
#> $model$capri_bic$probabilities$probabilities.fit$estimated.marginal.probs
#> [1] NA
#>
#> $model$capri_bic$probabilities$probabilities.fit$estimated.joint.probs
#> [1] NA
#>
#> $model$capri_bic$probabilities$probabilities.fit$estimated.conditional.probs
#> [1] NA
#>
#>
#>
#> $model$capri_bic$parents.pos
#> parents
#> gene 4 8
#> gene 5 7
#> gene 7 -1
#> gene 29 -1
#> gene 30 -1
#> gene 31 -1
#> gene 32 3
#> gene 33 -1
#> gene 34 27
#> gene 36 -1
#> gene 40 -1
#> gene 44 5
#> gene 47 24
#> gene 49 8
#> gene 50 27
#> gene 51 8
#> gene 52 -1
#> gene 53 5
#> gene 54 -1
#> gene 55 -1
#> gene 56 1
#> gene 66 24
#> gene 69 21
#> gene 77 -1
#> gene 88 -1
#> gene 89 -1
#> gene 91 4
#> gene 111 -1
#> XOR_EZH2 -1
#> OR_CSF3R -1
#>
#> $model$capri_bic$error.rates
#> $model$capri_bic$error.rates$error.fp
#> [1] NA
#>
#> $model$capri_bic$error.rates$error.fn
#> [1] NA
#>
#>
#> $model$capri_bic$adj.matrix
#> $model$capri_bic$adj.matrix$adj.matrix.pf
#> gene 4 gene 5 gene 7 gene 29 gene 30 gene 31 gene 32 gene 33 gene 34
#> gene 4 0 0 0 0 0 0 0 0 1
#> gene 5 0 0 0 0 0 0 0 0 0
#> gene 7 0 0 0 0 0 1 1 0 1
#> gene 29 0 0 0 0 1 0 0 0 1
#> gene 30 0 0 0 0 0 0 0 0 0
#> gene 31 0 0 0 0 0 0 0 0 0
#> gene 32 0 1 0 0 0 0 0 0 0
#> gene 33 1 0 0 0 1 0 0 0 1
#> gene 34 0 0 0 0 0 0 0 0 0
#> gene 36 0 0 0 0 0 0 0 0 0
#> gene 40 0 0 0 0 0 0 0 0 0
#> gene 44 0 0 0 0 0 0 0 0 0
#> gene 47 0 0 0 0 0 0 0 0 0
#> gene 49 0 0 0 0 0 0 0 0 0
#> gene 50 0 0 0 0 0 0 0 0 0
#> gene 51 0 0 0 0 0 0 0 0 0
#> gene 52 0 0 0 0 0 0 0 0 0
#> gene 53 0 0 0 0 0 0 0 0 0
#> gene 54 0 0 0 0 0 0 0 0 0
#> gene 55 0 0 0 0 0 0 1 0 0
#> gene 56 0 0 0 0 0 0 0 0 0
#> gene 66 0 0 0 0 0 0 0 0 0
#> gene 69 0 0 0 0 0 0 0 0 0
#> gene 77 0 0 0 0 0 0 0 0 0
#> gene 88 0 0 0 0 1 0 0 0 0
#> gene 89 0 0 0 0 0 0 0 0 0
#> gene 91 0 0 0 0 0 0 0 0 1
#> gene 111 0 0 0 0 0 0 0 0 0
#> XOR_EZH2 1 0 0 0 1 0 0 0 0
#> OR_CSF3R 0 0 0 0 0 0 1 0 0
#> gene 36 gene 40 gene 44 gene 47 gene 49 gene 50 gene 51 gene 52
#> gene 4 0 0 0 0 0 0 0 0
#> gene 5 0 0 0 0 0 0 0 0
#> gene 7 0 0 0 0 0 0 0 0
#> gene 29 0 0 1 0 0 1 0 0
#> gene 30 0 0 1 0 0 0 0 0
#> gene 31 0 0 0 0 0 0 0 0
#> gene 32 0 0 0 0 0 0 0 0
#> gene 33 0 0 0 0 1 0 1 0
#> gene 34 0 0 0 0 0 0 0 0
#> gene 36 0 0 0 0 0 0 0 0
#> gene 40 0 0 0 0 0 0 0 0
#> gene 44 0 0 0 0 0 0 0 0
#> gene 47 0 0 0 0 0 0 0 0
#> gene 49 0 0 0 0 0 0 0 0
#> gene 50 0 0 0 0 0 0 0 0
#> gene 51 0 0 0 0 0 0 0 0
#> gene 52 0 0 0 0 0 0 0 0
#> gene 53 0 0 0 0 0 0 0 0
#> gene 54 0 0 0 0 0 0 0 0
#> gene 55 0 0 0 0 0 0 0 0
#> gene 56 0 0 0 0 0 0 0 0
#> gene 66 0 0 0 0 0 0 0 0
#> gene 69 0 0 0 0 0 0 0 0
#> gene 77 0 0 0 1 0 0 0 0
#> gene 88 0 0 1 0 0 0 0 0
#> gene 89 0 0 0 0 0 0 0 0
#> gene 91 0 0 0 0 0 1 0 0
#> gene 111 0 0 0 0 0 0 0 0
#> XOR_EZH2 0 0 0 0 1 0 1 0
#> OR_CSF3R 0 0 0 0 0 0 0 0
#> gene 53 gene 54 gene 55 gene 56 gene 66 gene 69 gene 77 gene 88
#> gene 4 0 0 0 1 0 1 0 0
#> gene 5 0 0 0 0 0 0 0 0
#> gene 7 0 0 0 0 0 0 0 0
#> gene 29 0 0 1 0 0 0 0 1
#> gene 30 1 0 0 0 0 0 0 0
#> gene 31 0 0 0 0 0 0 0 0
#> gene 32 0 0 0 0 1 0 1 0
#> gene 33 1 0 0 1 0 0 0 0
#> gene 34 0 0 0 0 0 0 0 0
#> gene 36 0 0 0 0 0 0 0 0
#> gene 40 0 0 0 0 0 0 0 0
#> gene 44 0 0 0 0 0 0 0 0
#> gene 47 0 0 0 0 0 0 0 0
#> gene 49 0 0 0 0 0 0 0 0
#> gene 50 0 0 0 0 0 0 0 0
#> gene 51 0 0 0 0 0 0 0 0
#> gene 52 0 0 0 0 0 0 0 0
#> gene 53 0 0 0 0 0 0 0 0
#> gene 54 0 0 0 0 0 0 0 0
#> gene 55 0 0 0 0 1 0 1 0
#> gene 56 0 0 0 0 0 1 0 0
#> gene 66 0 0 0 0 0 0 0 0
#> gene 69 0 0 0 0 0 0 0 0
#> gene 77 0 0 0 0 1 0 0 0
#> gene 88 0 0 1 0 0 0 0 0
#> gene 89 0 0 0 0 0 0 0 0
#> gene 91 0 0 0 0 0 0 0 0
#> gene 111 0 0 0 0 0 0 0 0
#> XOR_EZH2 1 0 0 1 0 0 0 0
#> OR_CSF3R 0 0 0 0 1 0 1 0
#> gene 89 gene 91 gene 111 XOR_EZH2 OR_CSF3R
#> gene 4 0 0 0 0 0
#> gene 5 0 0 0 0 0
#> gene 7 0 0 0 0 0
#> gene 29 1 1 1 0 1
#> gene 30 0 0 0 0 0
#> gene 31 0 0 0 0 0
#> gene 32 0 0 0 0 0
#> gene 33 0 0 0 0 0
#> gene 34 0 0 0 0 0
#> gene 36 0 0 0 0 0
#> gene 40 0 0 0 0 0
#> gene 44 0 0 0 0 0
#> gene 47 0 0 0 0 0
#> gene 49 0 0 0 0 0
#> gene 50 0 0 0 0 0
#> gene 51 0 0 0 0 0
#> gene 52 0 0 0 0 0
#> gene 53 0 0 0 0 0
#> gene 54 0 0 0 0 0
#> gene 55 0 0 1 0 0
#> gene 56 0 0 0 0 0
#> gene 66 0 0 0 0 0
#> gene 69 0 0 0 0 0
#> gene 77 0 0 0 0 0
#> gene 88 0 0 0 0 0
#> gene 89 0 0 0 0 0
#> gene 91 0 0 0 0 0
#> gene 111 0 0 0 0 0
#> XOR_EZH2 0 0 0 0 0
#> OR_CSF3R 0 0 0 0 0
#>
#> $model$capri_bic$adj.matrix$adj.matrix.fit
#> gene 4 gene 5 gene 7 gene 29 gene 30 gene 31 gene 32 gene 33 gene 34
#> gene 4 0 0 0 0 0 0 0 0 0
#> gene 5 0 0 0 0 0 0 0 0 0
#> gene 7 0 0 0 0 0 0 1 0 0
#> gene 29 0 0 0 0 0 0 0 0 0
#> gene 30 0 0 0 0 0 0 0 0 0
#> gene 31 0 0 0 0 0 0 0 0 0
#> gene 32 0 1 0 0 0 0 0 0 0
#> gene 33 1 0 0 0 0 0 0 0 0
#> gene 34 0 0 0 0 0 0 0 0 0
#> gene 36 0 0 0 0 0 0 0 0 0
#> gene 40 0 0 0 0 0 0 0 0 0
#> gene 44 0 0 0 0 0 0 0 0 0
#> gene 47 0 0 0 0 0 0 0 0 0
#> gene 49 0 0 0 0 0 0 0 0 0
#> gene 50 0 0 0 0 0 0 0 0 0
#> gene 51 0 0 0 0 0 0 0 0 0
#> gene 52 0 0 0 0 0 0 0 0 0
#> gene 53 0 0 0 0 0 0 0 0 0
#> gene 54 0 0 0 0 0 0 0 0 0
#> gene 55 0 0 0 0 0 0 0 0 0
#> gene 56 0 0 0 0 0 0 0 0 0
#> gene 66 0 0 0 0 0 0 0 0 0
#> gene 69 0 0 0 0 0 0 0 0 0
#> gene 77 0 0 0 0 0 0 0 0 0
#> gene 88 0 0 0 0 0 0 0 0 0
#> gene 89 0 0 0 0 0 0 0 0 0
#> gene 91 0 0 0 0 0 0 0 0 1
#> gene 111 0 0 0 0 0 0 0 0 0
#> XOR_EZH2 0 0 0 0 0 0 0 0 0
#> OR_CSF3R 0 0 0 0 0 0 0 0 0
#> gene 36 gene 40 gene 44 gene 47 gene 49 gene 50 gene 51 gene 52
#> gene 4 0 0 0 0 0 0 0 0
#> gene 5 0 0 0 0 0 0 0 0
#> gene 7 0 0 0 0 0 0 0 0
#> gene 29 0 0 0 0 0 0 0 0
#> gene 30 0 0 1 0 0 0 0 0
#> gene 31 0 0 0 0 0 0 0 0
#> gene 32 0 0 0 0 0 0 0 0
#> gene 33 0 0 0 0 1 0 1 0
#> gene 34 0 0 0 0 0 0 0 0
#> gene 36 0 0 0 0 0 0 0 0
#> gene 40 0 0 0 0 0 0 0 0
#> gene 44 0 0 0 0 0 0 0 0
#> gene 47 0 0 0 0 0 0 0 0
#> gene 49 0 0 0 0 0 0 0 0
#> gene 50 0 0 0 0 0 0 0 0
#> gene 51 0 0 0 0 0 0 0 0
#> gene 52 0 0 0 0 0 0 0 0
#> gene 53 0 0 0 0 0 0 0 0
#> gene 54 0 0 0 0 0 0 0 0
#> gene 55 0 0 0 0 0 0 0 0
#> gene 56 0 0 0 0 0 0 0 0
#> gene 66 0 0 0 0 0 0 0 0
#> gene 69 0 0 0 0 0 0 0 0
#> gene 77 0 0 0 1 0 0 0 0
#> gene 88 0 0 0 0 0 0 0 0
#> gene 89 0 0 0 0 0 0 0 0
#> gene 91 0 0 0 0 0 1 0 0
#> gene 111 0 0 0 0 0 0 0 0
#> XOR_EZH2 0 0 0 0 0 0 0 0
#> OR_CSF3R 0 0 0 0 0 0 0 0
#> gene 53 gene 54 gene 55 gene 56 gene 66 gene 69 gene 77 gene 88
#> gene 4 0 0 0 1 0 0 0 0
#> gene 5 0 0 0 0 0 0 0 0
#> gene 7 0 0 0 0 0 0 0 0
#> gene 29 0 0 0 0 0 0 0 0
#> gene 30 1 0 0 0 0 0 0 0
#> gene 31 0 0 0 0 0 0 0 0
#> gene 32 0 0 0 0 0 0 0 0
#> gene 33 0 0 0 0 0 0 0 0
#> gene 34 0 0 0 0 0 0 0 0
#> gene 36 0 0 0 0 0 0 0 0
#> gene 40 0 0 0 0 0 0 0 0
#> gene 44 0 0 0 0 0 0 0 0
#> gene 47 0 0 0 0 0 0 0 0
#> gene 49 0 0 0 0 0 0 0 0
#> gene 50 0 0 0 0 0 0 0 0
#> gene 51 0 0 0 0 0 0 0 0
#> gene 52 0 0 0 0 0 0 0 0
#> gene 53 0 0 0 0 0 0 0 0
#> gene 54 0 0 0 0 0 0 0 0
#> gene 55 0 0 0 0 0 0 0 0
#> gene 56 0 0 0 0 0 1 0 0
#> gene 66 0 0 0 0 0 0 0 0
#> gene 69 0 0 0 0 0 0 0 0
#> gene 77 0 0 0 0 1 0 0 0
#> gene 88 0 0 0 0 0 0 0 0
#> gene 89 0 0 0 0 0 0 0 0
#> gene 91 0 0 0 0 0 0 0 0
#> gene 111 0 0 0 0 0 0 0 0
#> XOR_EZH2 0 0 0 0 0 0 0 0
#> OR_CSF3R 0 0 0 0 0 0 0 0
#> gene 89 gene 91 gene 111 XOR_EZH2 OR_CSF3R
#> gene 4 0 0 0 0 0
#> gene 5 0 0 0 0 0
#> gene 7 0 0 0 0 0
#> gene 29 0 1 0 0 0
#> gene 30 0 0 0 0 0
#> gene 31 0 0 0 0 0
#> gene 32 0 0 0 0 0
#> gene 33 0 0 0 0 0
#> gene 34 0 0 0 0 0
#> gene 36 0 0 0 0 0
#> gene 40 0 0 0 0 0
#> gene 44 0 0 0 0 0
#> gene 47 0 0 0 0 0
#> gene 49 0 0 0 0 0
#> gene 50 0 0 0 0 0
#> gene 51 0 0 0 0 0
#> gene 52 0 0 0 0 0
#> gene 53 0 0 0 0 0
#> gene 54 0 0 0 0 0
#> gene 55 0 0 0 0 0
#> gene 56 0 0 0 0 0
#> gene 66 0 0 0 0 0
#> gene 69 0 0 0 0 0
#> gene 77 0 0 0 0 0
#> gene 88 0 0 0 0 0
#> gene 89 0 0 0 0 0
#> gene 91 0 0 0 0 0
#> gene 111 0 0 0 0 0
#> XOR_EZH2 0 0 0 0 0
#> OR_CSF3R 0 0 0 0 0
#>
#>
#> $model$capri_bic$score
#> [1] -316.9889
#>
#> $model$capri_bic$logLik
#> [1] -235.8336
#>
#>
#> $model$capri_aic
#> $model$capri_aic$probabilities
#> $model$capri_aic$probabilities$probabilities.observed
#> $model$capri_aic$probabilities$probabilities.observed$marginal.probs
#> marginal probability
#> gene 4 0.07416667
#> gene 5 0.02946970
#> gene 7 0.16984848
#> gene 29 0.35257576
#> gene 30 0.07954545
#> gene 31 0.02962121
#> gene 32 0.07318182
#> gene 33 0.14984848
#> gene 34 0.07045455
#> gene 36 0.03295455
#> gene 40 0.02727273
#> gene 44 0.02916667
#> gene 47 0.02984848
#> gene 49 0.02750000
#> gene 50 0.03166667
#> gene 51 0.02954545
#> gene 52 0.03068182
#> gene 53 0.03166667
#> gene 54 0.03060606
#> gene 55 0.10598485
#> gene 56 0.05242424
#> gene 66 0.02886364
#> gene 69 0.02916667
#> gene 77 0.05113636
#> gene 88 0.12439394
#> gene 89 0.02810606
#> gene 91 0.10007576
#> gene 111 0.07856061
#> XOR_EZH2 0.19787879
#> OR_CSF3R 0.15500000
#>
#> $model$capri_aic$probabilities$probabilities.observed$joint.probs
#> gene 4 gene 5 gene 7 gene 29 gene 30 gene 31
#> gene 4 0.07348485 0.00000000 0.02272727 0.00000000 0.00000000 0.000
#> gene 5 0.00000000 0.02484848 0.02484848 0.00000000 0.00000000 0.000
#> gene 7 0.02272727 0.02484848 0.16984848 0.02439394 0.00000000 0.025
#> gene 29 0.00000000 0.00000000 0.02439394 0.35257576 0.05090909 0.000
#> gene 30 0.00000000 0.00000000 0.00000000 0.05090909 0.07909091 0.000
#> gene 31 0.00000000 0.00000000 0.02500000 0.00000000 0.00000000 0.025
#> gene 32 0.00000000 0.02484848 0.04863636 0.00000000 0.00000000 0.000
#> gene 33 0.04939394 0.00000000 0.04696970 0.00000000 0.02818182 0.000
#> gene 34 0.02272727 0.00000000 0.02272727 0.04727273 0.00000000 0.000
#> gene 36 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 40 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 44 0.00000000 0.00000000 0.00000000 0.02378788 0.02378788 0.000
#> gene 47 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 49 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 50 0.00000000 0.00000000 0.00000000 0.02742424 0.00000000 0.000
#> gene 51 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 52 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 53 0.00000000 0.00000000 0.00000000 0.00000000 0.02818182 0.000
#> gene 54 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 55 0.00000000 0.00000000 0.00000000 0.05590909 0.00000000 0.000
#> gene 56 0.05075758 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 66 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 69 0.02409091 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 77 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000
#> gene 88 0.00000000 0.00000000 0.02424242 0.05075758 0.02378788 0.000
#> gene 89 0.00000000 0.00000000 0.00000000 0.02318182 0.00000000 0.000
#> gene 91 0.00000000 0.00000000 0.00000000 0.10000000 0.00000000 0.000
#> gene 111 0.00000000 0.00000000 0.00000000 0.05287879 0.00000000 0.000
#> XOR_EZH2 0.04939394 0.02484848 0.07181818 0.02318182 0.02818182 0.000
#> OR_CSF3R 0.00000000 0.00000000 0.00000000 0.07984848 0.00000000 0.000
#> gene 32 gene 33 gene 34 gene 36 gene 40 gene 44
#> gene 4 0.00000000 0.04939394 0.02272727 0.00000000 0.00000000 0.00000000
#> gene 5 0.02484848 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 7 0.04863636 0.04696970 0.02272727 0.00000000 0.00000000 0.00000000
#> gene 29 0.00000000 0.00000000 0.04727273 0.00000000 0.00000000 0.02378788
#> gene 30 0.00000000 0.02818182 0.00000000 0.00000000 0.00000000 0.02378788
#> gene 31 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 32 0.07257576 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 33 0.00000000 0.14984848 0.02272727 0.00000000 0.00000000 0.00000000
#> gene 34 0.00000000 0.02272727 0.07000000 0.00000000 0.00000000 0.00000000
#> gene 36 0.00000000 0.00000000 0.00000000 0.02878788 0.00000000 0.00000000
#> gene 40 0.00000000 0.00000000 0.00000000 0.00000000 0.02212121 0.00000000
#> gene 44 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.02378788
#> gene 47 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 49 0.00000000 0.02257576 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 50 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 51 0.00000000 0.02545455 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 52 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 53 0.00000000 0.02818182 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 54 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 55 0.02393939 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 56 0.00000000 0.02666667 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 66 0.02393939 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 69 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 77 0.02393939 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 88 0.00000000 0.02424242 0.00000000 0.00000000 0.00000000 0.02378788
#> gene 89 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 91 0.00000000 0.00000000 0.04727273 0.00000000 0.00000000 0.00000000
#> gene 111 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> XOR_EZH2 0.02484848 0.14984848 0.02272727 0.00000000 0.00000000 0.00000000
#> OR_CSF3R 0.02393939 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 47 gene 49 gene 50 gene 51 gene 52 gene 53
#> gene 4 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 5 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 7 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 29 0.00000000 0.00000000 0.02742424 0.00000000 0.00000000 0.00000000
#> gene 30 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.02818182
#> gene 31 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 32 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 33 0.00000000 0.02257576 0.00000000 0.02545455 0.00000000 0.02818182
#> gene 34 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 36 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 40 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 44 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 47 0.02590909 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 49 0.00000000 0.02257576 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 50 0.00000000 0.00000000 0.02742424 0.00000000 0.00000000 0.00000000
#> gene 51 0.00000000 0.00000000 0.00000000 0.02545455 0.00000000 0.00000000
#> gene 52 0.00000000 0.00000000 0.00000000 0.00000000 0.02666667 0.00000000
#> gene 53 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.02818182
#> gene 54 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 55 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 56 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 66 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 69 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 77 0.02590909 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 88 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 89 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 91 0.00000000 0.00000000 0.02742424 0.00000000 0.00000000 0.00000000
#> gene 111 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> XOR_EZH2 0.00000000 0.02257576 0.00000000 0.02545455 0.00000000 0.02818182
#> OR_CSF3R 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 54 gene 55 gene 56 gene 66 gene 69 gene 77
#> gene 4 0.00000000 0.00000000 0.05075758 0.00000000 0.02409091 0.00000000
#> gene 5 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 7 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 29 0.00000000 0.05590909 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 30 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 31 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 32 0.00000000 0.02393939 0.00000000 0.02393939 0.00000000 0.02393939
#> gene 33 0.00000000 0.00000000 0.02666667 0.00000000 0.00000000 0.00000000
#> gene 34 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 36 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 40 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 44 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 47 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.02590909
#> gene 49 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 50 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 51 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 52 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 53 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 54 0.02575758 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 55 0.00000000 0.10590909 0.00000000 0.02393939 0.00000000 0.02393939
#> gene 56 0.00000000 0.00000000 0.05075758 0.00000000 0.02409091 0.00000000
#> gene 66 0.00000000 0.02393939 0.00000000 0.02393939 0.00000000 0.02393939
#> gene 69 0.00000000 0.00000000 0.02409091 0.00000000 0.02409091 0.00000000
#> gene 77 0.00000000 0.02393939 0.00000000 0.02393939 0.00000000 0.04984848
#> gene 88 0.00000000 0.02696970 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 89 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 91 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 111 0.00000000 0.02893939 0.00000000 0.00000000 0.00000000 0.00000000
#> XOR_EZH2 0.00000000 0.00000000 0.02666667 0.00000000 0.00000000 0.00000000
#> OR_CSF3R 0.00000000 0.10590909 0.00000000 0.02393939 0.00000000 0.02393939
#> gene 88 gene 89 gene 91 gene 111 XOR_EZH2 OR_CSF3R
#> gene 4 0.00000000 0.00000000 0.00000000 0.00000000 0.04939394 0.00000000
#> gene 5 0.00000000 0.00000000 0.00000000 0.00000000 0.02484848 0.00000000
#> gene 7 0.02424242 0.00000000 0.00000000 0.00000000 0.07181818 0.00000000
#> gene 29 0.05075758 0.02318182 0.10000000 0.05287879 0.02318182 0.07984848
#> gene 30 0.02378788 0.00000000 0.00000000 0.00000000 0.02818182 0.00000000
#> gene 31 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 32 0.00000000 0.00000000 0.00000000 0.00000000 0.02484848 0.02393939
#> gene 33 0.02424242 0.00000000 0.00000000 0.00000000 0.14984848 0.00000000
#> gene 34 0.00000000 0.00000000 0.04727273 0.00000000 0.02272727 0.00000000
#> gene 36 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 40 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 44 0.02378788 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 47 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 49 0.00000000 0.00000000 0.00000000 0.00000000 0.02257576 0.00000000
#> gene 50 0.00000000 0.00000000 0.02742424 0.00000000 0.00000000 0.00000000
#> gene 51 0.00000000 0.00000000 0.00000000 0.00000000 0.02545455 0.00000000
#> gene 52 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 53 0.00000000 0.00000000 0.00000000 0.00000000 0.02818182 0.00000000
#> gene 54 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 55 0.02696970 0.00000000 0.00000000 0.02893939 0.00000000 0.10590909
#> gene 56 0.00000000 0.00000000 0.00000000 0.00000000 0.02666667 0.00000000
#> gene 66 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.02393939
#> gene 69 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> gene 77 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.02393939
#> gene 88 0.12439394 0.00000000 0.00000000 0.00000000 0.02424242 0.02696970
#> gene 89 0.00000000 0.02318182 0.00000000 0.00000000 0.02318182 0.00000000
#> gene 91 0.00000000 0.00000000 0.10000000 0.00000000 0.00000000 0.00000000
#> gene 111 0.00000000 0.00000000 0.00000000 0.07803030 0.00000000 0.07803030
#> XOR_EZH2 0.02424242 0.02318182 0.00000000 0.00000000 0.19787879 0.00000000
#> OR_CSF3R 0.02696970 0.00000000 0.00000000 0.07803030 0.00000000 0.15500000
#>
#> $model$capri_aic$probabilities$probabilities.observed$conditional.probs
#> conditional probability
#> gene 4 0.3296259
#> gene 5 0.3395445
#> gene 7 1
#> gene 29 1
#> gene 30 1
#> gene 31 0.14719
#> gene 32 numeric,2
#> gene 33 1
#> gene 34 numeric,2
#> gene 36 1
#> gene 40 1
#> gene 44 0.2990476
#> gene 47 0.5066667
#> gene 49 0.1506572
#> gene 50 0.2740348
#> gene 51 0.1698686
#> gene 52 1
#> gene 53 0.3542857
#> gene 54 1
#> gene 55 1
#> gene 56 0.6843718
#> gene 66 0.4681481
#> gene 69 0.4595376
#> gene 77 numeric,2
#> gene 88 1
#> gene 89 0.06574989
#> gene 91 0.283627
#> gene 111 1
#> XOR_EZH2 1
#> OR_CSF3R 1
#>
#>
#> $model$capri_aic$probabilities$probabilities.fit
#> $model$capri_aic$probabilities$probabilities.fit$estimated.marginal.probs
#> [1] NA
#>
#> $model$capri_aic$probabilities$probabilities.fit$estimated.joint.probs
#> [1] NA
#>
#> $model$capri_aic$probabilities$probabilities.fit$estimated.conditional.probs
#> [1] NA
#>
#>
#>
#> $model$capri_aic$parents.pos
#> parents
#> gene 4 8
#> gene 5 7
#> gene 7 -1
#> gene 29 -1
#> gene 30 -1
#> gene 31 3
#> gene 32 integer,2
#> gene 33 -1
#> gene 34 integer,2
#> gene 36 -1
#> gene 40 -1
#> gene 44 5
#> gene 47 24
#> gene 49 8
#> gene 50 27
#> gene 51 8
#> gene 52 -1
#> gene 53 5
#> gene 54 -1
#> gene 55 -1
#> gene 56 1
#> gene 66 24
#> gene 69 21
#> gene 77 integer,2
#> gene 88 -1
#> gene 89 4
#> gene 91 4
#> gene 111 -1
#> XOR_EZH2 -1
#> OR_CSF3R -1
#>
#> $model$capri_aic$error.rates
#> $model$capri_aic$error.rates$error.fp
#> [1] NA
#>
#> $model$capri_aic$error.rates$error.fn
#> [1] NA
#>
#>
#> $model$capri_aic$adj.matrix
#> $model$capri_aic$adj.matrix$adj.matrix.pf
#> gene 4 gene 5 gene 7 gene 29 gene 30 gene 31 gene 32 gene 33 gene 34
#> gene 4 0 0 0 0 0 0 0 0 1
#> gene 5 0 0 0 0 0 0 0 0 0
#> gene 7 0 0 0 0 0 1 1 0 1
#> gene 29 0 0 0 0 1 0 0 0 1
#> gene 30 0 0 0 0 0 0 0 0 0
#> gene 31 0 0 0 0 0 0 0 0 0
#> gene 32 0 1 0 0 0 0 0 0 0
#> gene 33 1 0 0 0 1 0 0 0 1
#> gene 34 0 0 0 0 0 0 0 0 0
#> gene 36 0 0 0 0 0 0 0 0 0
#> gene 40 0 0 0 0 0 0 0 0 0
#> gene 44 0 0 0 0 0 0 0 0 0
#> gene 47 0 0 0 0 0 0 0 0 0
#> gene 49 0 0 0 0 0 0 0 0 0
#> gene 50 0 0 0 0 0 0 0 0 0
#> gene 51 0 0 0 0 0 0 0 0 0
#> gene 52 0 0 0 0 0 0 0 0 0
#> gene 53 0 0 0 0 0 0 0 0 0
#> gene 54 0 0 0 0 0 0 0 0 0
#> gene 55 0 0 0 0 0 0 1 0 0
#> gene 56 0 0 0 0 0 0 0 0 0
#> gene 66 0 0 0 0 0 0 0 0 0
#> gene 69 0 0 0 0 0 0 0 0 0
#> gene 77 0 0 0 0 0 0 0 0 0
#> gene 88 0 0 0 0 1 0 0 0 0
#> gene 89 0 0 0 0 0 0 0 0 0
#> gene 91 0 0 0 0 0 0 0 0 1
#> gene 111 0 0 0 0 0 0 0 0 0
#> XOR_EZH2 1 0 0 0 1 0 0 0 0
#> OR_CSF3R 0 0 0 0 0 0 1 0 0
#> gene 36 gene 40 gene 44 gene 47 gene 49 gene 50 gene 51 gene 52
#> gene 4 0 0 0 0 0 0 0 0
#> gene 5 0 0 0 0 0 0 0 0
#> gene 7 0 0 0 0 0 0 0 0
#> gene 29 0 0 1 0 0 1 0 0
#> gene 30 0 0 1 0 0 0 0 0
#> gene 31 0 0 0 0 0 0 0 0
#> gene 32 0 0 0 0 0 0 0 0
#> gene 33 0 0 0 0 1 0 1 0
#> gene 34 0 0 0 0 0 0 0 0
#> gene 36 0 0 0 0 0 0 0 0
#> gene 40 0 0 0 0 0 0 0 0
#> gene 44 0 0 0 0 0 0 0 0
#> gene 47 0 0 0 0 0 0 0 0
#> gene 49 0 0 0 0 0 0 0 0
#> gene 50 0 0 0 0 0 0 0 0
#> gene 51 0 0 0 0 0 0 0 0
#> gene 52 0 0 0 0 0 0 0 0
#> gene 53 0 0 0 0 0 0 0 0
#> gene 54 0 0 0 0 0 0 0 0
#> gene 55 0 0 0 0 0 0 0 0
#> gene 56 0 0 0 0 0 0 0 0
#> gene 66 0 0 0 0 0 0 0 0
#> gene 69 0 0 0 0 0 0 0 0
#> gene 77 0 0 0 1 0 0 0 0
#> gene 88 0 0 1 0 0 0 0 0
#> gene 89 0 0 0 0 0 0 0 0
#> gene 91 0 0 0 0 0 1 0 0
#> gene 111 0 0 0 0 0 0 0 0
#> XOR_EZH2 0 0 0 0 1 0 1 0
#> OR_CSF3R 0 0 0 0 0 0 0 0
#> gene 53 gene 54 gene 55 gene 56 gene 66 gene 69 gene 77 gene 88
#> gene 4 0 0 0 1 0 1 0 0
#> gene 5 0 0 0 0 0 0 0 0
#> gene 7 0 0 0 0 0 0 0 0
#> gene 29 0 0 1 0 0 0 0 1
#> gene 30 1 0 0 0 0 0 0 0
#> gene 31 0 0 0 0 0 0 0 0
#> gene 32 0 0 0 0 1 0 1 0
#> gene 33 1 0 0 1 0 0 0 0
#> gene 34 0 0 0 0 0 0 0 0
#> gene 36 0 0 0 0 0 0 0 0
#> gene 40 0 0 0 0 0 0 0 0
#> gene 44 0 0 0 0 0 0 0 0
#> gene 47 0 0 0 0 0 0 0 0
#> gene 49 0 0 0 0 0 0 0 0
#> gene 50 0 0 0 0 0 0 0 0
#> gene 51 0 0 0 0 0 0 0 0
#> gene 52 0 0 0 0 0 0 0 0
#> gene 53 0 0 0 0 0 0 0 0
#> gene 54 0 0 0 0 0 0 0 0
#> gene 55 0 0 0 0 1 0 1 0
#> gene 56 0 0 0 0 0 1 0 0
#> gene 66 0 0 0 0 0 0 0 0
#> gene 69 0 0 0 0 0 0 0 0
#> gene 77 0 0 0 0 1 0 0 0
#> gene 88 0 0 1 0 0 0 0 0
#> gene 89 0 0 0 0 0 0 0 0
#> gene 91 0 0 0 0 0 0 0 0
#> gene 111 0 0 0 0 0 0 0 0
#> XOR_EZH2 1 0 0 1 0 0 0 0
#> OR_CSF3R 0 0 0 0 1 0 1 0
#> gene 89 gene 91 gene 111 XOR_EZH2 OR_CSF3R
#> gene 4 0 0 0 0 0
#> gene 5 0 0 0 0 0
#> gene 7 0 0 0 0 0
#> gene 29 1 1 1 0 1
#> gene 30 0 0 0 0 0
#> gene 31 0 0 0 0 0
#> gene 32 0 0 0 0 0
#> gene 33 0 0 0 0 0
#> gene 34 0 0 0 0 0
#> gene 36 0 0 0 0 0
#> gene 40 0 0 0 0 0
#> gene 44 0 0 0 0 0
#> gene 47 0 0 0 0 0
#> gene 49 0 0 0 0 0
#> gene 50 0 0 0 0 0
#> gene 51 0 0 0 0 0
#> gene 52 0 0 0 0 0
#> gene 53 0 0 0 0 0
#> gene 54 0 0 0 0 0
#> gene 55 0 0 1 0 0
#> gene 56 0 0 0 0 0
#> gene 66 0 0 0 0 0
#> gene 69 0 0 0 0 0
#> gene 77 0 0 0 0 0
#> gene 88 0 0 0 0 0
#> gene 89 0 0 0 0 0
#> gene 91 0 0 0 0 0
#> gene 111 0 0 0 0 0
#> XOR_EZH2 0 0 0 0 0
#> OR_CSF3R 0 0 0 0 0
#>
#> $model$capri_aic$adj.matrix$adj.matrix.fit
#> gene 4 gene 5 gene 7 gene 29 gene 30 gene 31 gene 32 gene 33 gene 34
#> gene 4 0 0 0 0 0 0 0 0 1
#> gene 5 0 0 0 0 0 0 0 0 0
#> gene 7 0 0 0 0 0 1 1 0 0
#> gene 29 0 0 0 0 0 0 0 0 0
#> gene 30 0 0 0 0 0 0 0 0 0
#> gene 31 0 0 0 0 0 0 0 0 0
#> gene 32 0 1 0 0 0 0 0 0 0
#> gene 33 1 0 0 0 0 0 0 0 0
#> gene 34 0 0 0 0 0 0 0 0 0
#> gene 36 0 0 0 0 0 0 0 0 0
#> gene 40 0 0 0 0 0 0 0 0 0
#> gene 44 0 0 0 0 0 0 0 0 0
#> gene 47 0 0 0 0 0 0 0 0 0
#> gene 49 0 0 0 0 0 0 0 0 0
#> gene 50 0 0 0 0 0 0 0 0 0
#> gene 51 0 0 0 0 0 0 0 0 0
#> gene 52 0 0 0 0 0 0 0 0 0
#> gene 53 0 0 0 0 0 0 0 0 0
#> gene 54 0 0 0 0 0 0 0 0 0
#> gene 55 0 0 0 0 0 0 1 0 0
#> gene 56 0 0 0 0 0 0 0 0 0
#> gene 66 0 0 0 0 0 0 0 0 0
#> gene 69 0 0 0 0 0 0 0 0 0
#> gene 77 0 0 0 0 0 0 0 0 0
#> gene 88 0 0 0 0 0 0 0 0 0
#> gene 89 0 0 0 0 0 0 0 0 0
#> gene 91 0 0 0 0 0 0 0 0 1
#> gene 111 0 0 0 0 0 0 0 0 0
#> XOR_EZH2 0 0 0 0 0 0 0 0 0
#> OR_CSF3R 0 0 0 0 0 0 0 0 0
#> gene 36 gene 40 gene 44 gene 47 gene 49 gene 50 gene 51 gene 52
#> gene 4 0 0 0 0 0 0 0 0
#> gene 5 0 0 0 0 0 0 0 0
#> gene 7 0 0 0 0 0 0 0 0
#> gene 29 0 0 0 0 0 0 0 0
#> gene 30 0 0 1 0 0 0 0 0
#> gene 31 0 0 0 0 0 0 0 0
#> gene 32 0 0 0 0 0 0 0 0
#> gene 33 0 0 0 0 1 0 1 0
#> gene 34 0 0 0 0 0 0 0 0
#> gene 36 0 0 0 0 0 0 0 0
#> gene 40 0 0 0 0 0 0 0 0
#> gene 44 0 0 0 0 0 0 0 0
#> gene 47 0 0 0 0 0 0 0 0
#> gene 49 0 0 0 0 0 0 0 0
#> gene 50 0 0 0 0 0 0 0 0
#> gene 51 0 0 0 0 0 0 0 0
#> gene 52 0 0 0 0 0 0 0 0
#> gene 53 0 0 0 0 0 0 0 0
#> gene 54 0 0 0 0 0 0 0 0
#> gene 55 0 0 0 0 0 0 0 0
#> gene 56 0 0 0 0 0 0 0 0
#> gene 66 0 0 0 0 0 0 0 0
#> gene 69 0 0 0 0 0 0 0 0
#> gene 77 0 0 0 1 0 0 0 0
#> gene 88 0 0 0 0 0 0 0 0
#> gene 89 0 0 0 0 0 0 0 0
#> gene 91 0 0 0 0 0 1 0 0
#> gene 111 0 0 0 0 0 0 0 0
#> XOR_EZH2 0 0 0 0 0 0 0 0
#> OR_CSF3R 0 0 0 0 0 0 0 0
#> gene 53 gene 54 gene 55 gene 56 gene 66 gene 69 gene 77 gene 88
#> gene 4 0 0 0 1 0 0 0 0
#> gene 5 0 0 0 0 0 0 0 0
#> gene 7 0 0 0 0 0 0 0 0
#> gene 29 0 0 0 0 0 0 0 0
#> gene 30 1 0 0 0 0 0 0 0
#> gene 31 0 0 0 0 0 0 0 0
#> gene 32 0 0 0 0 0 0 1 0
#> gene 33 0 0 0 0 0 0 0 0
#> gene 34 0 0 0 0 0 0 0 0
#> gene 36 0 0 0 0 0 0 0 0
#> gene 40 0 0 0 0 0 0 0 0
#> gene 44 0 0 0 0 0 0 0 0
#> gene 47 0 0 0 0 0 0 0 0
#> gene 49 0 0 0 0 0 0 0 0
#> gene 50 0 0 0 0 0 0 0 0
#> gene 51 0 0 0 0 0 0 0 0
#> gene 52 0 0 0 0 0 0 0 0
#> gene 53 0 0 0 0 0 0 0 0
#> gene 54 0 0 0 0 0 0 0 0
#> gene 55 0 0 0 0 0 0 0 0
#> gene 56 0 0 0 0 0 1 0 0
#> gene 66 0 0 0 0 0 0 0 0
#> gene 69 0 0 0 0 0 0 0 0
#> gene 77 0 0 0 0 1 0 0 0
#> gene 88 0 0 0 0 0 0 0 0
#> gene 89 0 0 0 0 0 0 0 0
#> gene 91 0 0 0 0 0 0 0 0
#> gene 111 0 0 0 0 0 0 0 0
#> XOR_EZH2 0 0 0 0 0 0 0 0
#> OR_CSF3R 0 0 0 0 0 0 1 0
#> gene 89 gene 91 gene 111 XOR_EZH2 OR_CSF3R
#> gene 4 0 0 0 0 0
#> gene 5 0 0 0 0 0
#> gene 7 0 0 0 0 0
#> gene 29 1 1 0 0 0
#> gene 30 0 0 0 0 0
#> gene 31 0 0 0 0 0
#> gene 32 0 0 0 0 0
#> gene 33 0 0 0 0 0
#> gene 34 0 0 0 0 0
#> gene 36 0 0 0 0 0
#> gene 40 0 0 0 0 0
#> gene 44 0 0 0 0 0
#> gene 47 0 0 0 0 0
#> gene 49 0 0 0 0 0
#> gene 50 0 0 0 0 0
#> gene 51 0 0 0 0 0
#> gene 52 0 0 0 0 0
#> gene 53 0 0 0 0 0
#> gene 54 0 0 0 0 0
#> gene 55 0 0 0 0 0
#> gene 56 0 0 0 0 0
#> gene 66 0 0 0 0 0
#> gene 69 0 0 0 0 0
#> gene 77 0 0 0 0 0
#> gene 88 0 0 0 0 0
#> gene 89 0 0 0 0 0
#> gene 91 0 0 0 0 0
#> gene 111 0 0 0 0 0
#> XOR_EZH2 0 0 0 0 0
#> OR_CSF3R 0 0 0 0 0
#>
#>
#> $model$capri_aic$score
#> [1] -277.5718
#>
#> $model$capri_aic$logLik
#> [1] -224.5718
#>
#>
#>
#> $parameters
#> $parameters$algorithm
#> [1] "CAPRI"
#>
#> $parameters$command
#> [1] "hc"
#>
#> $parameters$regularization
#> [1] "bic" "aic"
#>
#> $parameters$do.boot
#> [1] TRUE
#>
#> $parameters$nboot
#> [1] 100
#>
#> $parameters$pvalue
#> [1] 0.05
#>
#> $parameters$min.boot
#> [1] 3
#>
#> $parameters$min.stat
#> [1] TRUE
#>
#> $parameters$boot.seed
#> NULL
#>
#> $parameters$silent
#> [1] FALSE
#>
#> $parameters$error.rates
#> $parameters$error.rates$epos
#> [1] 0
#>
#> $parameters$error.rates$eneg
#> [1] 0
#>
#>
#>
#> $execution.time
#> user system elapsed
#> 8.081 0.194 8.184
#>
#> $kfold
#> $kfold$capri_bic
#> $kfold$capri_bic$bn.kcv.list
#>
#> k-fold cross-validation for Bayesian networks
#>
#> target network structure:
#> [ins_del ASXL1][missense_point_mutations SETBP1]
#> [missense_point_mutations NRAS_Ex2_3][missense_point_mutations KRAS_Ex2_3]
#> [missense_point_mutations EZH2][missense_point_mutations IDH2_R140]
#> [missense_point_mutations SF3B1_Ex_12_15][missense_point_mutations GATA2]
#> [missense_point_mutations MTA2][missense_point_mutations CSF3R]
#> [nonsense_ins_del CEBPA][nonsense_point_mutations TET2]
#> [nonsense_point_mutations EZH2][nonsense_point_mutations CSF3R]
#> [Pattern XOR_EZH2][Pattern OR_CSF3R]
#> [ins_del TET2|missense_point_mutations EZH2]
#> [missense_point_mutations TET2|ins_del ASXL1]
#> [missense_point_mutations JARID_2_Ex1_18|missense_point_mutations NRAS_Ex2_3]
#> [missense_point_mutations EED_Ex2_12|nonsense_ins_del CEBPA]
#> [missense_point_mutations CEBPA|missense_point_mutations EZH2]
#> [missense_point_mutations ETNK1|missense_point_mutations EZH2]
#> [missense_point_mutations IRAK4|missense_point_mutations NRAS_Ex2_3]
#> [nonsense_ins_del WT1|nonsense_ins_del CEBPA]
#> [nonsense_point_mutations ASXL1|missense_point_mutations SETBP1]
#> [ins_del EZH2|missense_point_mutations TET2]
#> [missense_point_mutations CBL_Ex_8_9|nonsense_point_mutations ASXL1]
#> [missense_point_mutations EPHB3|nonsense_point_mutations ASXL1]
#> [missense_point_mutations KIT|ins_del TET2]
#> [nonsense_ins_del RUNX_1|missense_point_mutations KIT]
#> number of folds: 2
#> loss function: Log-Likelihood Loss (disc.)
#> number of runs: 2
#> average loss over the runs: 7.414657
#> standard deviation of the loss: 0.04683479
#>
#>
#> $kfold$capri_bic$eloss
#> [1] 7.447774 7.381539
#>
#>
#> $kfold$capri_aic
#> $kfold$capri_aic$bn.kcv.list
#>
#> k-fold cross-validation for Bayesian networks
#>
#> target network structure:
#> [ins_del ASXL1][missense_point_mutations SETBP1]
#> [missense_point_mutations NRAS_Ex2_3][missense_point_mutations EZH2]
#> [missense_point_mutations IDH2_R140][missense_point_mutations SF3B1_Ex_12_15]
#> [missense_point_mutations GATA2][missense_point_mutations MTA2]
#> [missense_point_mutations CSF3R][nonsense_point_mutations TET2]
#> [nonsense_point_mutations CSF3R][Pattern XOR_EZH2][Pattern OR_CSF3R]
#> [ins_del TET2|missense_point_mutations EZH2]
#> [missense_point_mutations KRAS_Ex2_3|ins_del ASXL1]
#> [missense_point_mutations TET2|ins_del ASXL1:missense_point_mutations CSF3R]
#> [missense_point_mutations JARID_2_Ex1_18|missense_point_mutations NRAS_Ex2_3]
#> [missense_point_mutations CEBPA|missense_point_mutations EZH2]
#> [missense_point_mutations ETNK1|missense_point_mutations EZH2]
#> [missense_point_mutations IRAK4|missense_point_mutations NRAS_Ex2_3]
#> [nonsense_point_mutations EZH2|missense_point_mutations SETBP1]
#> [nonsense_point_mutations ASXL1|missense_point_mutations SETBP1]
#> [ins_del EZH2|missense_point_mutations TET2]
#> [missense_point_mutations CBL_Ex_8_9|ins_del TET2:nonsense_point_mutations ASXL1]
#> [missense_point_mutations EPHB3|nonsense_point_mutations ASXL1]
#> [missense_point_mutations KIT|ins_del TET2]
#> [nonsense_ins_del CEBPA|missense_point_mutations TET2:Pattern OR_CSF3R]
#> [missense_point_mutations EED_Ex2_12|nonsense_ins_del CEBPA]
#> [nonsense_ins_del WT1|nonsense_ins_del CEBPA]
#> [nonsense_ins_del RUNX_1|missense_point_mutations KIT]
#> number of folds: 2
#> loss function: Log-Likelihood Loss (disc.)
#> number of runs: 2
#> average loss over the runs: 6.973349
#> standard deviation of the loss: 0.1433313
#>
#>
#> $kfold$capri_aic$eloss
#> [1] 7.074699 6.871998
#>
#>
#>