Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling

Diaz-Uriarte, Ramon

doi:10.1186/s12859-015-0466-7

Table 5 Ranking of all 144 combinations of method, filtering, and sampling scheme (time, type) when drivers are unknown with respect to each performance measure

From: Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling

Method and sampling	Conjunction				No conjunction
	Diff	PFD	PND	FPF	Diff	PFD	PND	FPF
S5, OT-A, last, singleC	1	7	15	60	1	13	13	60
S5, OT-A, last, wholeT_0.5	2	6	23	59	2	7	23	59
J5, OT-A, last, wholeT_0.01	3	1	26	71	4	2	29	74
S5, OT-A, last, wholeT_0.01	4	2	2	94	3	5	4	94
S5, OT-A, unif, wholeT_0.01	5	17	33	69	10	17	32.5	68.5
S5, OT, unif, singleC	6	41	61.5	28	9	38	55.5	20.5
S5, OT-A, unif, singleC	7	50	61.5	31	8	49	55.5	20.5
J1, OT-A, last, singleC	8	15	38	80	6	12	37	75
J1, OT-A, last, wholeT_0.5	9	10	39	79	7	6	39	71
S5, OT-A, unif, wholeT_0.5	10	47	67	29.5	14	45	60.5	27.5
S5, OT, unif, wholeT_0.01	11	11	34	68	11	10	32.5	68.5
J1, OT-A, last, wholeT_0.01	13	21	9	109	15	19	8	108
S1, OT-A, last, wholeT_0.5	18	39	3	117	5	27	3	116
S1, OT-A, last, singleC	21	38	4	120	12	32	2	120
S5, OT, last, singleC	23	16	51	21	20	8	42	19
S5, OT, last, wholeT_0.5	24	3	55	16	23	3	49	17
J1, OT, unif, wholeT_0.01	29	9	36	91	30	14	36	91
S5, CBN-A, unif, wholeT_0.01	30	4	37	89	40	20	40	103
J5, OT, last, wholeT_0.01	31	5	59	32	36	4	62	50
S1, OT-A, last, wholeT_0.01	36	48	1	134	24	50	1	134
S5, OT, last, wholeT_0.01	38	8	29	83	34	1	24	82
J1, OT, last, wholeT_0.5	47	14	89	61	38	9	83	43
J5, OT, last, singleC	48	35	101	4	58	43	109	4.5
J5, DiP-A, unif, singleC	49	125	139	10.5	51	128	138	9
J5, OT, last, wholeT_0.5	57	20	102	4	75	23	112	4.5
J5, DiP, unif, singleC	61	131	143	8	60	132	144	4.5
J5, DiP, unif, wholeT_0.5	64	144	144	4	64	144	143	4.5
J5, DiP, last, singleC	79	115	140	4	81	119	140	4.5
J5, DiP, last, wholeT_0.5	82	137	138	4	83	136	139	4.5
S5, DiP, last, wholeT_0.5	83	134	120	9	87	130	110	10
J1, DiP, last, wholeT_0.5	91	132	134	4	89	134	134	4.5
J1, DiP, last, singleC	92	110	135	4	93	115	132	4.5
S1, OT-A, unif, wholeT_0.01	102	65	5	136	70	59	5	136
S1, OT, unif, wholeT_0.01	109	62	6	135	74	55	6	135
S1, CBN-A, unif, wholeT_0.01	137	82	7	143	140	81	7	143
S1, CBN-A, last, wholeT_0.01	142	93	10	137	139	94	12	137
S1, CBN, unif, wholeT_0.01	143	84	8	144	143	90	9	144

Methods have been ordered by their performance in the first performance measure. Best 10 methods are shown in bold. Only methods that are within the best 10 in at least one performance measure are shown (full table as well as tables split by S.Size are available from Additional file 2).

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com

BMC Bioinformatics

Contact us