Skip to main content

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 γ=99.9% vs FREEC   PG with γ=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.