Skip to main content

Table 1 Estimation the transition parameters and the states

From: A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays

   True r
True p Estimation 0.001 0.01 0.05 0.1
  p 0.00115 0.00104 0.00101 0.00107
0.001 r 0.00108 0.01028 0.04889 0.09462
  Accuracy 0.99965 0.99893 0.99487 0.99227
  p 0.00959 0.00994 0.00934 0.01006
0.01 r 0.00112 0.01057 0.04931 0.09588
  Accuracy 0.99725 0.99622 0.99303 0.98850
  p 0.04861 0.04831 0.04794 0.04849
0.05 r 0.00109 0.01034 0.04812 0.09402
  Accuracy 0.99180 0.99000 0.98517 0.98018
  p 0.09551 0.09356 0.09603 0.09300
0.1 r 0.00140 0.01006 0.04857 0.09480
  Accuracy 0.99233 0.98980 0.98269 0.97708
  1. For each pair of true p and r parameters, we simulated six samples where all SNPs were given a heterozygous call in the germline DNA. Here we report the average of the estimation for p and r and how often the true copy-number state is recovered.