Simulate phenotypes in a number of regions

given region coordinates (locus), the function extracts genotypes for all loci in that region, constructs genotypes matrix G (applies imputation and fixes allele encoding) and computes maf per marker.

sim_y_in_regions(
  regions,
  vcf_file,
  n_markers,
  get_betas_fun = rnorm_betas,
  get_betas_args = list(mean = 0, sd = 1),
  rare = T,
  frac_negative = 0,
  thr = 0.01,
  force_silent = T,
  seed = 42,
  e_mean = 0,
  e_sd = 1,
  GP_map = c(0, 1, 2)
)

Arguments

regions	list of regions to use.
vcf_file	character, path to vcf file containing genotypes.
n_markers	integer, number of markers to use in the simulation (see [get_effects()]).
get_betas_fun	see [get_effects()].
get_betas_args	see [get_effects()].
rare	see [get_effects()].
frac_negative	see [get_effects()].
thr	see get_effects.
force_silent	logical, if `TRUE` seqminer verbosity will be silenced (may cause some issues on non-*nix machines).
seed	see get_effects.
e_mean	numeric, mean error.
e_sd	numeric, error std. dev.
GP_map	vector of genotype-phenotype map values for `AA`, `aA` and `aa` respectively.

Value

list with genotypes matrix and maf vector

Author

Marcin Kierczak marcin.kierczak@scilifelab.se