Performs a simulation with multiple replicates for a pre-specified set of arguments.
CSeQTL_oneExtremeSim(
NN,
MAF,
true_BETA0,
true_KAPPA,
true_ETA,
true_PHI = 0.1,
wRHO,
noiseRHO = 0,
RR = 50,
vec_MARG = c(TRUE, FALSE),
vec_TRIM = c(TRUE, FALSE),
vec_PERM = c(TRUE, FALSE),
thres_TRIM = 10,
ncores = 1,
sim_fn
)A R list containing the results of a small-scale simulation.
res contains replicate-specific results while ures contains
overall simulation results include power, frequency of replicates with
constrained eta estimates and gene expressions inferred to be zero after optimization.
Positive integer for sample size.
Positive numeric value between 0 and 1 for the minor allele frequency to simulate phased SNP genotypes assuming Hardy-Weinberg.
A positive numeric value denoting the reference cell type
and reference base's expression multiplied by two and log transformed.
For example, if the TReC for reference base and cell type is 500, then
true_BETA0 = log{2 * 500}.
A numeric vector denoting the baseline fold change in TReC between a cell type and reference. By definition, the first element is 1.
A numeric vector where each element denotes the fold change in TReC between the non-reference and reference base in a cell type.
A non-negative numeric value denoting the over-dispersion term
associated with TReC. If true_PHI > 0, TReC is simulated with the
negative binomial. If true_PHI = 0, TReC is simulated with the poisson.
Takes integer values 1, 2, or 3 to simulate three scenarios of cell type proportions.
A positive numeric value to purposely distort simulated cell type compositions.
A positive integer for number of replicates to generate and analyze.
A boolean vector for marginal and/or cell type-specific analyses to be run. By default, both sets of analyses are run.
A boolean vector for whether or not analyses with trimmed outcomes are included. By default, both sets of analyses are run.
A boolean vector for whether or not permuted SNP analyses are included. By default, both sets of analyses are run.
A positive numeric value to perform subject outcome trimming. Subjects with standardized Cooks' Distances greater than the threshold are trimmed.
A positive integer specifying the number of threads available to decrease computational runtime.
Character value specifying the full path and filename to store intermediate simulation replicates should errors arise.