exploreQTL {polyqtlR}

Explore the possible segregation type of a QTL peak using Schwarz Information Criterion

Description

Function to explore the possible segregation type at a QTL position using the Schwarz Information Criterion

Usage

exploreQTL(
  IBD_list,
  Phenotype.df,
  genotype.ID,
  trait.ID,
  linkage_group,
  LOD_data,
  cM = NULL,
  QTLconfig = NULL,
  plotBIC = TRUE,
  deltaBIC = 6,
  testAllele_Effects = TRUE,
  log = NULL
)

Arguments

IBD_list

List of IBD probabilities

Phenotype.df

A data.frame containing phenotypic values

genotype.ID

The colname of Phenotype.df that contains the population identifiers (F1 names) (must be a colname of Phenotype.df)

trait.ID

The colname of Phenotype.df that contains the response variable to use in the model (must be a colname of Phenotype.df)

linkage_group

Numeric identifier of the linkage group being tested, based on the order of IBD_list. Only a single linkage group is allowed.

LOD_data

Output of QTLscan function

cM

By default NULL, in which case the position of maximum LOD score is taken as the position of interest. Otherwise, the cM position to be explored.

QTLconfig

Nested list of homologue configurations and modes of action of QTL to be explored and compared, the output of segMaker. Note that a default List is available of all possible bi-allelic QTL if none is provided. Each list element is itself a list with components

homs :

a vector of length at least 1, describing the proposed homologues the functional allele Q is on

mode :

Vector of same length as homs with codes "a" for additive and "d" for dominant.

plotBIC

Logical, with default TRUE - should the calculated BIC values be plotted?

deltaBIC

Numeric, by default 6. Configurations within this distance of the minimum BIC are considered plausible.

testAllele_Effects

Logical, with default TRUE - should the effects of the different alleles be tested using the most likely QTL configuration?

log

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Value

List with the following items:

linkage_group

Linkage group of the QTL peak being explored

cM

CentiMorgan position of the locus being explored

BIC

Vector of BIC values corresponding to elements of QTLconfig provided for testing

Allele.effects

Summary of the means and standard errors of groups with (+) and without(-) the specified allele combinations for the most likely QTLconfig if testAllele_Effects = TRUE (NULL otherwise).

genotype.means

A one-column matrix of mean phenotype values of offspring classes, with rownames corresponding to the genotype class. If the probability of certain genotype classes is 0 (e.g. double reduction classes where no double reduction occurred), then the genotype mean for that class will be NA

Examples

data("IBD_4x","BLUEs.pheno","qtl_LODs.4x")
exploreQTL(IBD_list = IBD_4x,
           Phenotype.df = BLUEs.pheno,
           genotype.ID = "Geno",
           trait.ID = "BLUE",
           linkage_group = 1,
           LOD_data = qtl_LODs.4x)