eqtlPlot: Plot Expressions for Genotype groups

Description

This function plots expression value boxplots, grouped for the different genotypes.

Usage

eqtlPlot(snp=NULL, gene=NULL, eqtl=NULL,geno=NULL,gex=NULL, genoSamples=NULL)

Arguments

snp

Grouping SNP.

gene

Expression values of a gene.

eqtl

An eQTL object.

geno

An genotype object.

gex

An gene expression object.

genoSamples

Sample names of the genotype object.

Value

A Figure with three boxplots, giving the expressions for the three genotype groups.

Details

This function can be used to plot the expression values of a certain gene and grouped with one SNP. This can be done after an eQTL is performed. In that case just the eqtl object has to be given. If no eQTL has been performed previous than the plot can be created be giving the objects geno, gex and genoSamples instead, see eQTL.

The gene options gives the name of the gene whos expression values should be used and snp whos SNPs genotypes.

Currently only the eQTL option is implemented.

Examples

Run this code

# First perform an eQTL
# lm.myEQTL <- eQTL(gex=ourExpression, geno=genotData, xAnnot=xAnnotDF, windowSize=1, genoSamples=genoSamples, method="LM")

# eqtlPlot(snp="RS1928123", gene="ARLTS", eqtl=lm.myEQTL)