Returns a dataframe with all the selective advantage relations in a
TRONCO model. Confidence is also shown - see as.confidence. It is possible to
specify a subset of events or models if multiple reconstruction have
been performed.
All the selective advantage relations in a TRONCO model
data(test_model)
as.selective.advantage.relations(test_model)
#> $capri_bic
#> SELECTS SELECTED
#> 1 ins_del TET2 missense_point_mutations KIT
#> 2 ins_del ASXL1 missense_point_mutations TET2
#> 3 missense_point_mutations SETBP1 nonsense_point_mutations ASXL1
#> 4 missense_point_mutations NRAS_Ex2_3 missense_point_mutations JARID_2_Ex1_18
#> 5 missense_point_mutations NRAS_Ex2_3 missense_point_mutations IRAK4
#> 6 missense_point_mutations TET2 ins_del EZH2
#> 7 missense_point_mutations EZH2 ins_del TET2
#> 8 missense_point_mutations EZH2 missense_point_mutations CEBPA
#> 9 missense_point_mutations EZH2 missense_point_mutations ETNK1
#> 10 missense_point_mutations KIT nonsense_ins_del RUNX_1
#> 11 nonsense_ins_del CEBPA missense_point_mutations EED_Ex2_12
#> 12 nonsense_ins_del CEBPA nonsense_ins_del WT1
#> 13 nonsense_point_mutations ASXL1 missense_point_mutations CBL_Ex_8_9
#> 14 nonsense_point_mutations ASXL1 missense_point_mutations EPHB3
#> OBS.SELECTS OBS.SELECTED TEMPORAL.PRIORITY PROBABILITY.RAISING
#> 1 3 2 1.421229e-06 5.460128e-22
#> 2 7 3 2.278343e-38 6.442772e-35
#> 3 14 4 1.426321e-55 7.635188e-63
#> 4 3 1 1.056706e-31 2.612641e-09
#> 5 3 1 2.827924e-29 1.055365e-20
#> 6 3 1 1.282066e-25 1.177708e-10
#> 7 6 3 9.373014e-28 7.840153e-28
#> 8 6 1 1.677847e-53 1.835656e-14
#> 9 6 1 8.126240e-53 2.348033e-21
#> 10 2 1 2.540051e-13 3.228035e-03
#> 11 2 1 4.511947e-12 1.966262e-07
#> 12 2 1 2.157029e-13 9.434522e-05
#> 13 4 3 1.650994e-08 2.926887e-32
#> 14 4 1 1.661066e-39 6.448439e-17
#> HYPERGEOMETRIC
#> 1 0.00000000
#> 2 0.07368421
#> 3 0.00000000
#> 4 0.07500000
#> 5 0.00000000
#> 6 0.07500000
#> 7 0.05364372
#> 8 0.15000000
#> 9 0.00000000
#> 10 0.05000000
#> 11 0.00000000
#> 12 0.05000000
#> 13 0.02226721
#> 14 0.00000000
#>
#> $capri_aic
#> SELECTS SELECTED
#> 1 ins_del TET2 missense_point_mutations CBL_Ex_8_9
#> 2 ins_del TET2 missense_point_mutations KIT
#> 3 ins_del ASXL1 missense_point_mutations KRAS_Ex2_3
#> 4 ins_del ASXL1 missense_point_mutations TET2
#> 5 missense_point_mutations SETBP1 nonsense_point_mutations EZH2
#> 6 missense_point_mutations SETBP1 nonsense_point_mutations ASXL1
#> 7 missense_point_mutations NRAS_Ex2_3 missense_point_mutations JARID_2_Ex1_18
#> 8 missense_point_mutations NRAS_Ex2_3 missense_point_mutations IRAK4
#> 9 missense_point_mutations TET2 ins_del EZH2
#> 10 missense_point_mutations TET2 nonsense_ins_del CEBPA
#> 11 missense_point_mutations EZH2 ins_del TET2
#> 12 missense_point_mutations EZH2 missense_point_mutations CEBPA
#> 13 missense_point_mutations EZH2 missense_point_mutations ETNK1
#> 14 missense_point_mutations CSF3R missense_point_mutations TET2
#> 15 missense_point_mutations KIT nonsense_ins_del RUNX_1
#> 16 nonsense_ins_del CEBPA missense_point_mutations EED_Ex2_12
#> 17 nonsense_ins_del CEBPA nonsense_ins_del WT1
#> 18 nonsense_point_mutations ASXL1 missense_point_mutations CBL_Ex_8_9
#> 19 nonsense_point_mutations ASXL1 missense_point_mutations EPHB3
#> 20 Pattern OR_CSF3R nonsense_ins_del CEBPA
#> OBS.SELECTS OBS.SELECTED TEMPORAL.PRIORITY PROBABILITY.RAISING
#> 1 3 3 2.359743e-01 1.587286e-02
#> 2 3 2 1.421229e-06 5.460128e-22
#> 3 7 1 4.356112e-55 5.627097e-17
#> 4 7 3 2.278343e-38 6.442772e-35
#> 5 14 1 8.806722e-57 1.839890e-14
#> 6 14 4 1.426321e-55 7.635188e-63
#> 7 3 1 1.056706e-31 2.612641e-09
#> 8 3 1 2.827924e-29 1.055365e-20
#> 9 3 1 1.282066e-25 1.177708e-10
#> 10 3 2 5.985653e-07 1.056504e-05
#> 11 6 3 9.373014e-28 7.840153e-28
#> 12 6 1 1.677847e-53 1.835656e-14
#> 13 6 1 8.126240e-53 2.348033e-21
#> 14 4 3 5.618501e-11 6.632068e-05
#> 15 2 1 2.540051e-13 3.228035e-03
#> 16 2 1 4.511947e-12 1.966262e-07
#> 17 2 1 2.157029e-13 9.434522e-05
#> 18 4 3 1.650994e-08 2.926887e-32
#> 19 4 1 1.661066e-39 6.448439e-17
#> 20 6 2 7.398044e-44 2.822865e-06
#> HYPERGEOMETRIC
#> 1 0.21356275
#> 2 0.00000000
#> 3 0.00000000
#> 4 0.07368421
#> 5 0.35000000
#> 6 0.00000000
#> 7 0.07500000
#> 8 0.00000000
#> 9 0.07500000
#> 10 0.14615385
#> 11 0.05364372
#> 12 0.15000000
#> 13 0.00000000
#> 14 0.27732794
#> 15 0.05000000
#> 16 0.00000000
#> 17 0.05000000
#> 18 0.02226721
#> 19 0.00000000
#> 20 0.28076923
#>
as.selective.advantage.relations(test_model, events=as.events(test_model)[5:15,])
#> $capri_bic
#> SELECTS SELECTED
#> 1 missense_point_mutations NRAS_Ex2_3 missense_point_mutations JARID_2_Ex1_18
#> 2 missense_point_mutations EZH2 missense_point_mutations CEBPA
#> OBS.SELECTS OBS.SELECTED TEMPORAL.PRIORITY PROBABILITY.RAISING HYPERGEOMETRIC
#> 1 3 1 1.056706e-31 2.612641e-09 0.075
#> 2 6 1 1.677847e-53 1.835656e-14 0.150
#>
#> $capri_aic
#> SELECTS SELECTED
#> 1 missense_point_mutations NRAS_Ex2_3 missense_point_mutations JARID_2_Ex1_18
#> 2 missense_point_mutations EZH2 missense_point_mutations CEBPA
#> OBS.SELECTS OBS.SELECTED TEMPORAL.PRIORITY PROBABILITY.RAISING HYPERGEOMETRIC
#> 1 3 1 1.056706e-31 2.612641e-09 0.075
#> 2 6 1 1.677847e-53 1.835656e-14 0.150
#>
as.selective.advantage.relations(test_model, events=as.events(test_model)[5:15,], type='pf')
#> $pf
#> SELECTS SELECTED
#> 1 ins_del TET2 missense_point_mutations CBL_Ex_8_9
#> 2 ins_del TET2 missense_point_mutations KIT
#> 3 ins_del TET2 nonsense_ins_del RUNX_1
#> 4 ins_del ASXL1 missense_point_mutations KRAS_Ex2_3
#> 5 ins_del ASXL1 missense_point_mutations TET2
#> 6 ins_del ASXL1 missense_point_mutations CBL_Ex_8_9
#> 7 missense_point_mutations SETBP1 missense_point_mutations NRAS_Ex2_3
#> 8 missense_point_mutations SETBP1 missense_point_mutations CBL_Ex_8_9
#> 9 missense_point_mutations SETBP1 missense_point_mutations JARID_2_Ex1_18
#> 10 missense_point_mutations SETBP1 missense_point_mutations EPHB3
#> 11 missense_point_mutations SETBP1 missense_point_mutations CSF3R
#> 12 missense_point_mutations SETBP1 nonsense_point_mutations TET2
#> 13 missense_point_mutations SETBP1 nonsense_point_mutations EZH2
#> 14 missense_point_mutations SETBP1 nonsense_point_mutations ASXL1
#> 15 missense_point_mutations SETBP1 nonsense_point_mutations CSF3R
#> 16 missense_point_mutations SETBP1 Pattern OR_CSF3R
#> 17 missense_point_mutations NRAS_Ex2_3 missense_point_mutations JARID_2_Ex1_18
#> 18 missense_point_mutations NRAS_Ex2_3 missense_point_mutations IRAK4
#> 19 missense_point_mutations TET2 ins_del EZH2
#> 20 missense_point_mutations TET2 nonsense_ins_del WT1
#> 21 missense_point_mutations TET2 nonsense_ins_del CEBPA
#> 22 missense_point_mutations EZH2 ins_del TET2
#> 23 missense_point_mutations EZH2 missense_point_mutations NRAS_Ex2_3
#> 24 missense_point_mutations EZH2 missense_point_mutations CBL_Ex_8_9
#> 25 missense_point_mutations EZH2 missense_point_mutations CEBPA
#> 26 missense_point_mutations EZH2 missense_point_mutations ETNK1
#> 27 missense_point_mutations EZH2 missense_point_mutations IRAK4
#> 28 missense_point_mutations EZH2 missense_point_mutations KIT
#> 29 missense_point_mutations CSF3R missense_point_mutations TET2
#> 30 missense_point_mutations CSF3R nonsense_ins_del WT1
#> 31 missense_point_mutations CSF3R nonsense_ins_del CEBPA
#> 32 missense_point_mutations CSF3R nonsense_point_mutations CSF3R
#> 33 missense_point_mutations KIT nonsense_ins_del RUNX_1
#> 34 nonsense_ins_del CEBPA missense_point_mutations EED_Ex2_12
#> 35 nonsense_ins_del CEBPA nonsense_ins_del WT1
#> 36 nonsense_point_mutations TET2 missense_point_mutations NRAS_Ex2_3
#> 37 nonsense_point_mutations TET2 missense_point_mutations JARID_2_Ex1_18
#> 38 nonsense_point_mutations TET2 missense_point_mutations CSF3R
#> 39 nonsense_point_mutations ASXL1 missense_point_mutations CBL_Ex_8_9
#> 40 nonsense_point_mutations ASXL1 missense_point_mutations EPHB3
#> 41 Pattern XOR_EZH2 ins_del TET2
#> 42 Pattern XOR_EZH2 missense_point_mutations NRAS_Ex2_3
#> 43 Pattern XOR_EZH2 missense_point_mutations CEBPA
#> 44 Pattern XOR_EZH2 missense_point_mutations ETNK1
#> 45 Pattern XOR_EZH2 missense_point_mutations IRAK4
#> 46 Pattern XOR_EZH2 missense_point_mutations KIT
#> 47 Pattern OR_CSF3R missense_point_mutations TET2
#> 48 Pattern OR_CSF3R nonsense_ins_del WT1
#> 49 Pattern OR_CSF3R nonsense_ins_del CEBPA
#> OBS.SELECTS OBS.SELECTED TEMPORAL.PRIORITY PROBABILITY.RAISING
#> 1 3 3 2.359743e-01 1.587286e-02
#> 2 3 2 1.421229e-06 5.460128e-22
#> 3 3 1 3.262925e-27 5.352680e-07
#> 4 7 1 4.356112e-55 5.627097e-17
#> 5 7 3 2.278343e-38 6.442772e-35
#> 6 7 3 4.899826e-40 4.004727e-02
#> 7 14 3 4.357290e-56 7.755853e-24
#> 8 14 3 4.145089e-56 7.691348e-28
#> 9 14 1 9.175701e-57 5.311779e-11
#> 10 14 1 1.287253e-56 2.607680e-20
#> 11 14 4 6.828657e-56 5.697137e-19
#> 12 14 5 5.185189e-55 3.729102e-03
#> 13 14 1 8.806722e-57 1.839890e-14
#> 14 14 4 1.426321e-55 7.635188e-63
#> 15 14 3 3.972375e-56 3.011047e-32
#> 16 14 6 5.477097e-53 8.260024e-23
#> 17 3 1 1.056706e-31 2.612641e-09
#> 18 3 1 2.827924e-29 1.055365e-20
#> 19 3 1 1.282066e-25 1.177708e-10
#> 20 3 1 1.806902e-26 3.254703e-10
#> 21 3 2 5.985653e-07 1.056504e-05
#> 22 6 3 9.373014e-28 7.840153e-28
#> 23 6 3 3.120373e-25 8.401800e-13
#> 24 6 3 3.690851e-30 2.969062e-02
#> 25 6 1 1.677847e-53 1.835656e-14
#> 26 6 1 8.126240e-53 2.348033e-21
#> 27 6 1 3.167398e-52 3.631082e-27
#> 28 6 2 5.489839e-41 8.185249e-09
#> 29 4 3 5.618501e-11 6.632068e-05
#> 30 4 1 3.309532e-45 1.348268e-12
#> 31 4 2 1.860213e-26 3.703793e-06
#> 32 4 3 9.416075e-09 6.601609e-13
#> 33 2 1 2.540051e-13 3.228035e-03
#> 34 2 1 4.511947e-12 1.966262e-07
#> 35 2 1 2.157029e-13 9.434522e-05
#> 36 5 3 9.388325e-16 8.545585e-03
#> 37 5 1 4.217177e-49 3.823050e-10
#> 38 5 4 5.771054e-04 1.704655e-06
#> 39 4 3 1.650994e-08 2.926887e-32
#> 40 4 1 1.661066e-39 6.448439e-17
#> 41 8 3 1.657722e-44 8.907302e-28
#> 42 8 3 1.100280e-43 3.527613e-10
#> 43 8 1 2.432208e-56 1.836811e-14
#> 44 8 1 3.987969e-56 1.051434e-21
#> 45 8 1 4.919078e-56 1.589068e-27
#> 46 8 2 4.242942e-52 8.546011e-09
#> 47 6 3 4.947292e-32 2.296749e-04
#> 48 6 1 1.058573e-52 1.598725e-13
#> 49 6 2 7.398044e-44 2.822865e-06
#> HYPERGEOMETRIC
#> 1 0.21356275
#> 2 0.00000000
#> 3 0.07500000
#> 4 0.00000000
#> 5 0.07368421
#> 6 0.44777328
#> 7 0.03684211
#> 8 0.27631579
#> 9 0.35000000
#> 10 0.00000000
#> 11 0.11450925
#> 12 0.22238028
#> 13 0.35000000
#> 14 0.00000000
#> 15 0.03684211
#> 16 0.09909910
#> 17 0.07500000
#> 18 0.00000000
#> 19 0.07500000
#> 20 0.07500000
#> 21 0.14615385
#> 22 0.05364372
#> 23 0.05364372
#> 24 0.39433198
#> 25 0.15000000
#> 26 0.00000000
#> 27 0.00000000
#> 28 0.01923077
#> 29 0.27732794
#> 30 0.10000000
#> 31 0.19230769
#> 32 0.02226721
#> 33 0.05000000
#> 34 0.00000000
#> 35 0.05000000
#> 36 0.33755061
#> 37 0.12500000
#> 38 0.06899004
#> 39 0.02226721
#> 40 0.00000000
#> 41 0.09635628
#> 42 0.09635628
#> 43 0.20000000
#> 44 0.00000000
#> 45 0.00000000
#> 46 0.03589744
#> 47 0.39433198
#> 48 0.15000000
#> 49 0.28076923
#>