visualiseQTLeffects | R Documentation |
Function to visualise the effect of parental homologues around a QTL peak across the population.
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
)
IBD_list |
List of IBD probabilities |
Phenotype.df |
A data.frame containing phenotypic values |
genotype.ID |
The colname of |
trait.ID |
The colname of |
linkage_group |
Numeric identifier of the linkage group being tested, based on the order of |
LOD_data |
Output of |
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 |
allelic_interaction |
By default |
exploreQTL_output |
If |
return_plotData |
Logical, by default |
The estimated effects of the homologues, used in the visualisation
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)
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