Comparison of the number of lung cancer related regions that are identified by the six methods on the lung adenocarcinoma dataset.

<p>Comparison of the number of lung cancer related regions that are identified by the six methods on the lung adenocarcinoma dataset.</p

Methods evaluated in this comparison study.

<p>For the “peel-off” column, ‘Yes’ and ‘No’ indicate whether the methods adopt peel-off procedure.</p

FHSA-SED: Two-Locus Model Detection for Genome-Wide Association Study with Harmony Search Algorithm - Fig 4

<p>The power comparison on three DME models: (a) The left figure is the multiplicative model (H2 = 0.005); (b) The middle figure is threshold model (H2 = 0.02); (c) The right figure is the concrete model (H2 = 0.02).</p

Type I error rate comparison of the six methods.

<p>Amplification and deletion are tested separately, and the corresponding results are figured with red and blue bars; the type I error rate of 0.05 is represented by the dashed line in the figure.</p

Local search algorithm based on two-dimensional tabu table (TT).

<p>In Fig 2, X_i is the i^th SNP locus, '1' denote the two-locus model has been evaluated. '0' is otherwise.</p

The flow chart of FHSA-SED algorithm.

<p>① Yellow ellipse consists of the entire two-SNP combinations that have not been filtered. ② Orange ellipse contains the two-locus models with highest K2-score, which are the filtered results in 1^st stage. ③ Light green ellipse contains the two-locus models with highest Gini-score, which are the filtered results in 1^st stage. ④ Pink ellipse is the union of HM1 and HM2. ⑤ Final output results which have passed the G-test are in white ellipse.</p

Gene-gene network.

<p>The gene in Fig 13 is mapped from SNP, each SNP loci corresponds to a gene. A gene contains one or more SNPs, for example, <i>'rs380390'</i> and <i>'rs1329428'</i> are all mapped in gene: CFH.</p

The rate of somatic CNA across the genome and the frequency of somatic CNA across the samples in a set of segmented lung cancer profiles.

<p>Here we use log₂-ratios 0.322 (2.5 copies) and −0.415 (1.5 copies) to define amplifications and deletions. (a) The average rates of CNA for amplification and deletion among the 371 samples are 0.0379 and 0.0417, respectively. (b) A large part of amplifications and deletions are less than 0.1 in terms of frequency.</p

Comparison of memory usages for the six methods.

<p>Memory usage is depicted as a function of genome size when setting the sample size to 50, and is then depicted as a function of sample size when setting the genome size to 2000.</p

The statistical box plots of FHSA-SED algorithm.

<p>Illustrating the distribution of evaluation times and computation time (s). (1) The left figure illustrates the statistical distribution of evaluation times for 12 DME models for 100*5 datasets (100 datasets for each model, and FHSA-SED runs 5 times repeatedly for each data set). (2) The right figure illustrates the corresponding statistical distribution of computation times.</p