scan_multi_oneqtl_perm {qtl2pleio}

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

Description

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

Usage

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