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Table 1 Parameters tested for the seven R packages

From: A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array

Packages Parameters tested
Tuned packages   Tuning parameter Values tested Other parameters
  FASeg Sig 0.25, 0.1, 0.075, 0.05, 0.025, 0.01, 0.005, 0.001, 0.0001, 0.00001 Default
  aCGH Vr 10, 7, 5, 2, 1, 0.5, 0.1, 0.05, 0.01, 0.001 Default
  DNAcopy alpha 0.25, 0.1, 0.075, 0.05, 0.025, 0.01, 0.005, 0.001,0.0005, 0.0001 * nperm = 1000
  GLAD qlambda 0.75, 0.9, 0.925, 0.95, 0.975, 0.99, 0.9925, 0.995, 0.9975, 0.999 ** lambdabreak = 0.01
lambdacluster = 0.01
lambdaclusterGen = 0.01
param = c(d = 1)
Packages examined at default setting Picard Maxk = max(true segment size) + 5, maxSeg= #(true segments) + 1
  RJaCGH *** burnin = 50, *** TOT = 500, jump.parameters = NULL, k.max = #(true states) + 1
  BioHMM Default
  1. * The change in the number of permutations is to reduce computing time. Experiments showed that reducing the number from 10000 to 1000 has minimal effect on the outcome.
  2. ** These parameters were tuned according to the GLAD manual to increase sensitivity. Using default values, the method detected limited number of edges from noisy data.
  3. *** The purpose of reducing the number of iterations was to save computing time.