scan1: Single QTL scan

In jendelman/diaQTL: QTL Analysis in Diallel Populations

Single QTL scan

Description

Performs a linear regression for each position in the map.

Usage

scan1(
  data,
  trait,
  params = list(burnIn = 100, nIter = 1000),
  dominance = 1,
  covariate = NULL,
  chrom = NULL,
  n.core = 1
)

Arguments

data	variable of class diallel_geno_pheno
trait	name of trait
params	list containing burnIn and nIter
dominance	maximum dominance for the scan, see Details
covariate	optional, to include markers as covariates. See Details
chrom	names of chromosomes to scan (default is all)
n.core	number of cores for parallel execution

Details

Parameter dominance has possible values of 1 = additive, 2 = digenic dominance, 3 = trigenic dominance, 4 = quadrigenic dominance. MCMC params can be estimated using set_params. Optional argument covariate is used to include other markers in the model during the scan, which can improve statistical power with multiple QTL. It is a data frame with three columns: marker = name of the marker, dominance = 1 to 4, and epistasis = TRUE/FALSE. Function returns deltaDIC = DIC for the QTL model relative to null model with only GCA effects for the parents, as well as LL = posterior mean of the log-likelihood, which is used by BayesCI.

Value

Data frame containing the map, LL, and deltaDIC.

Examples

## Not run: 
## getting minimum burnIn and nIter
  set_params(data = diallel_example,
             trait = "tuber_shape")
                      
  scan1_example <- scan1(data = diallel_example,
                         chrom = "10",
                         trait = "tuber_shape",
                         params = list(burnIn=60,nIter=600))

## End(Not run)

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