Generate data for simulation analysis

Generate data for simulation analysis

make_data(
  num,
  anno,
  fn,
  lb.maf = 0.05,
  ub.maf = 0.5,
  filter.geno = TRUE,
  sd,
  b0 = 0,
  sigma = 1,
  ranef = FALSE,
  sigma.u = NULL,
  kinship = NULL,
  seed = 1
)

Arguments

num

A named, ordered integer vector specifying the numbers of simulations in the eight model categories. The model names in the correct order can be obtained using get_model_names.

anno

A data frame containing sample IDs (character strings or integers), subject IDs (character strings or integers), and treatment conditions (0 or 1). The columns must be names as "sample", "subject", and "condition".

fn

A character string specifying the function. This must be one of "nonlinear" and "linear", corresponding to nonlinear and linear models, respectively.

lb.maf

A scalar specifying the lower bound of MAF.

ub.maf

A scalar specifying the upper bound of MAF.

filter.geno

A Boolean variable as to whether to ensure that all genotype levels have at least one observation.

sd

A vetor of length three specifying the effect size standard deviations.

b0

A scalar specifying the intercept.

sigma

A scalar specifying the residual error standard deviation.

ranef

A Boolean variable as to whether to include random effect.

sigma.u

A scalar specifying the random intercept standard deviation. If ranef is TRUE, this is set to sqrt(0.2) by default.

kinship

A matrix containing pairwise genetic relatedness between subjects. The row and column names must match the set of unique elements of the "subject" column in "anno" in the corresponding order (i.e., unique(anno$subject)). This is set to NULL by default, in which case the identity matrix is used.

seed

A seed for RNG.

Value

A list of lists containing:

• y - A vector of phenotypes.

• g - A vector of genotypes.

• t - A vector of treatment indicators.

• subject - A vector of subject.

• index - An integer specifying one of the eight model. The order of models corresponding to the indices dan be obtained using get_model_names.

• maf - A scalar specifying the minor allele frequency used for generating the genotype data.

• beta - A named numeric vector specifying the true coefficient values used for generating the phenotype data. The "b0" element represents the intercept. The "b1", "b2", and "b3" elements respectively represent the genotype, treatment, and interaction effect sizes.