Keep only the first 12 character of samples barcode if there are no duplicates
TCGA.shorten.barcodes(x)A TRONCO compliant dataset
data(test_dataset)
TCGA.shorten.barcodes(test_dataset)
#> $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
#>
#>
#>