Return all genotypes for input 'x', which should be a TRONCO compliant dataset
see is.compliant.
Function keysToNames can be used to translate colnames to events.
as.genotypes(x)A TRONCO genotypes matrix.
data(test_dataset)
as.genotypes(test_dataset)
#> 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