pxg.plot: Phenotype by genotype plot at a single marker.

In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

Phenotype by genotype plot at a single marker.

Description

This function plots the phenotype versus the most probable genotype at a single marker.

Usage

  pxg.plot(pheno, pheno.col, probs, snp.id, snps, legend = TRUE, sex = NA, covar, ...)

Arguments

pheno	Data.frame containing the phenotype data with samples in rows and phenotypes in columns. Sample IDs in rownames and phenotype names in colnames.
pheno.col	Numeric or character vector: Either a vector of number that indicate columns to use or a set of column names in pheno.
probs	3D numeric array, containing the founder haplotype contributions or genotype probabilities. The sample IDs, founder letter codes and markers IDs must be in dimnames.
snp.id	Character string containing the marker to plot at. Must be in SNPs and dimnames(probs)[[3]].
snps	Data.frame containing 4 columns with marker location information. SNP ID, chr, Mb, cM in columns 1 through 4, respectively.
legend	Boolean that is true if a legend explaining the founder letter codes should be plotted.
sex	Character that is either FALSE or M, indicating sex. This is used only when the SNP ID is on the X chromosome and all of the samples are male. In this case, there are only 8 genotype states.
covar	Vector of categories for each sample (i.e. diet, treatement, etc.) which will be plotted as different symbols. Optional.
...	Additional arguments passed along to plot.

Details

The most probable genotype is inferred from the eight founder allelic contributions at the marker. If a founder has a value > 0.75, it is assumed to be homozygous.

Value

Creates a plot with the phenotype on the y-axis and the 36 DO genotypes on the x-axis.

Author(s)

Daniel Gatti

See Also

plot.doqtl, coefplot

Examples

  ## Not run:  pxg.plot(pheno, pheno.col, founder.probs, snp.id, snps) 

dmgatti/DOQTL documentation built on April 7, 2024, 10:35 p.m.