exploreQTL: Explore the possible segregation type of a QTL peak using...
In polyqtlR: QTL Analysis in Autopolyploid Bi-Parental F1 Populations

Description Usage Arguments Value Examples

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

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
)

`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.

List with the following items:

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).

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)