polyqtlR (version 0.1.1)

visualiseQTLeffects: Visualise QTL homologue effects around a QTL position

Description

Function to visualise the effect of parental homologues around a QTL peak across the population.

Usage

visualiseQTLeffects(
  IBD_list,
  Phenotype.df,
  genotype.ID,
  trait.ID,
  linkage_group,
  LOD_data,
  cM_range = NULL,
  col.pal = c("purple4", "white", "seagreen"),
  point.density = 50,
  zero.sum = FALSE,
  allelic_interaction = FALSE,
  exploreQTL_output = NULL,
  return_plotData = FALSE
)

Value

The estimated effects of the homologues, used in the visualisation

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_range

If required, the plotting region can be restricted to a specified range of centiMorgan positions (provided as a vector of start and end positions).

col.pal

Vector of colours to use in the visualisations (it is best to provide two or three colours for simplicity). By default, effects will be coloured from purple to green through white.

point.density

Parameter to increase the smoothing of homologue effect tracks

zero.sum

How allele substitution effect should be defined. If FALSE (by default), the effect of each homologue is computed relative to the overall phenotypic mean, otherwise contrasts (against offspring without the inherited homologue) are used.

allelic_interaction

By default FALSE, in which case the additive effects of parental alleles are visualised. If TRUE, a plot of the mean effect of combinations of parental alleles is visualised instead. exploreQTL_output is required in this case.

exploreQTL_output

If allelic_interaction = TRUE, the output of the function exploreQTL must be provided.

return_plotData

Logical, by default FALSE. If TRUE, plot data is returned, otherwise NULL.

Examples

data("IBD_4x","BLUEs.pheno","qtl_LODs.4x")
visualiseQTLeffects(IBD_list = IBD_4x,
                    Phenotype.df = BLUEs.pheno,
                    genotype.ID = "Geno",
                    trait.ID = "BLUE",
                    linkage_group = 2,
                    LOD_data = qtl_LODs.4x)