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Table 4 Hits shared and exclusively detected by the Poisson-Gamma (PG) model, the FREEC and the cn.MOPS approaches

From: A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data

  

PG with Îł=99.9% vs FREEC

 

PG with Îł=99.9% vs cn.MOPS

CNV

Sample

S PG − FREEC

E PG

E FREEC

 

S PG − cn.MOPS

E PG

E cn.MOPS

Deletions

HB3

175 (55.2)

130 (41.0)

12 (3.8)

 

195 (63.5)

110 (35.8)

2 (0.7)

 

DD2

175 (63.9)

90 (32.8)

9 (3.3)

 

152 (57.4)

113 (42.6)

0 (0.0)

 

7G8

81 (29.1)

124 (44.6)

73 (26.3)

 

120 (21.4)

85 (15.1)

357 (63.5)

 

GB4

72 (27.4)

181 (68.8)

10 (3.8)

 

150 (50.0)

103 (34.3)

47 (15.7)

 

OX005

153 (51.0)

121 (40.3)

26 (8.7)

 

205 (69.3)

69 (23.3)

22 (7.4)

 

OX006

93 (55.0)

74 (43.8)

2 (1.2)

 

62 (37.1)

105 (62.9)

0 (0.0)

Amplifications

HB3

19 (29.7)

41 (64.1)

4 (6.3)

 

23 (12.2)

37 (19.7)

128 (68.1)

 

DD2

586 (84.3)

48 (6.9)

61 (8.8)

 

608 (85.2)

26 (3.6)

80 (11.2)

 

7G8

187 (37.6)

28 (5.6)

283 (56.8)

 

212 (17.8)

3 (0.3)

973 (81.9)

 

GB4

6 (10.5)

41 (71.9)

10 (17.5)

 

38 (11.8)

9 (2.8)

274 (85.4)

 

OX005

62 (4.2)

130 (8.8)

1291 (87.1)

 

168 (5.7)

24 (0.8)

2473 (93.5)

 

OX006

27 (22.9)

63 (53.4)

28 (23.7)

 

64 (20.9)

26 (8.5)

216 (70.6)

  1. The frequencies (and the respective percentages in brackets) refer to the number of hits shared and exclusively detected by the PG model against FREEC and cn.MOPS, whereS PG-FREEC andS PG-cn.MOPS denote the hits shared between the respective pair of methods,E PG ,E FREEC andE cn.MOPS denote the exclusive hits produced by the corresponding methodology in the respective comparison. Percentages are in relation to the overall number of deletions and amplifications identified by the respective pair of methods.