Since both resting-state fMRI dataset (Baltimore dataset) and task-based fMRI dataset (false belief fMRI dataset) are fully sampled, we simulated undersampled k-space data ({mathbf{Y }}) in (2) by computing the Fourier transform of Casorati matrix ({mathbf{X }}) and then, retrospectively undersampling in the k-space using measurement matrix ({mathbf {Phi }}).
To evaluate different demographic scenarios (e.g. constant population sizes or population expansion from the time of the prehistoric sample), we simulated an extant sample and a prehistoric sample using the program COMPASS [ 17].
To estimate the fraction of amino-acid mutations that would have been sampled, we simulated randomly selecting 85% of the mutant codons from the HA sequence, and determined that these codons encoded ≈97% of the amino-acid mutations.
For each sample, we simulated 10 million and 30 million 100-bp single-end (CAST and DO) or paired-end (CAST only) reads with a standard error model (0.028% average mutations per sequence, 34.96 quality).
In each sample, we simulate, clonal expansions, each marked by a variable number t of mutations,.
For each dataset, and for a range of sub-sample sample sizes, we simulated a case control study and the two two-phase designs described above.
To account for variation in sample size, we simulated the actual distribution of sample sizes in the observed data.
In order to understand the relative benefit of increasing the number of loci versus increasing the sample size, we simulated bottlenecks with an N1 = 300 and a N2 = 50 using two radically different sampling strategies: One maximizing the number of individuals (i.e. using a sample size equal to N2) but using only 10 loci and another using 50 loci but only 10 individuals.
For each CG site in each simulated sample, we then simulated the reads (C if methylated or T if unmethylated) based on the average methylation level (Pm) from all real samples at this CG site.
To assess the performance of CLImAT for complex tumor samples, we generate simulated tumor samples with different impurity and ploidy.
