visualiseQTLeffects: Visualise QTL homologue effects around a QTL position

In polyqtlR: QTL Analysis in Autopolyploid Bi-Parental F1 Populations

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,
  return_plotData = FALSE
)

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

Value

The estimated effects of the homologues, used in the visualisation

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)

polyqtlR documentation built on Feb. 2, 2022, 5:09 p.m.