Permute the phenotypes matrix and then scan the genome. Record the genomewide greatest LOD score for each permuted data set.

Permute the phenotypes matrix and then scan the genome. Record the genomewide greatest LOD score for each permuted data set.

scan_multi_oneqtl_perm(
  probs_list,
  pheno,
  kinship_list = NULL,
  addcovar = NULL,
  n_perm = 1,
  cores = 1
)

Arguments

probs_list	a list of founder allele probabilities, one array per chromosome
pheno	a matrix of trait values
kinship_list	a list of kinship matrices, one per chromosome
addcovar	a matrix of covariate values
n_perm	positive integer for the number of permuted data sets to scan.
cores	number of cores for parallelization

Value

a vector of `n_perm` max lod statistics