scan1_permute: Permutation test for scan1

In jendelman/diaQTL: QTL Analysis in Diallel Populations

Permutation test for scan1

Description

Permutation test for scan1

Usage

scan1_permute(
  data,
  trait,
  params,
  n.permute = 1000,
  chrom = NULL,
  dominance = 1,
  covariate = NULL,
  n.core = 1
)

Arguments

data	Variable of class diallel_geno_pheno
trait	Name of trait
params	List containing burnIn and nIter
n.permute	Number of permutations
chrom	Names of chromosomes to scan (default is all)
dominance	Dominance degree (1-4)
covariate	optional, to include markers as covariates. See Details.
n.core	Number of cores for parallel execution

Value

Data frame with maximum LOD and minimum deltaDIC for each iteration

Examples

## Not run: 
  set_params(data = diallel_example,
             trait = "tuber_shape")
                      
  ans1_permut <- scan1_permute(data = diallel_example,
                               chrom = 10,
                               trait = "tuber_shape",
                               params = list(burnIn=60,nIter=600),
                               n.permute = 100)
                               
  ## computing permutation threshold for alpha=0.05                            
  quantile(ans1_permut$min_deltaDIC, 0.05)
                             

## End(Not run)

jendelman/diaQTL documentation built on Jan. 27, 2024, 6:39 a.m.