GGBase (version 3.34.0)

plot_EvG: display the association between expression values and genotypes in an smlSet instance

Description

display the association between expression values and genotypes in an smlSet instance

Usage

plot_EvG(gsym, rsid, sms, ...)

Arguments

gsym

instance of class genesym or probeId, casting a string that names a gene (which will be looked up using the annotation slot of sms) or a probe which must be resident on the array underlying the expression content of sms

rsid

instance of class rsid naming a SNP with genotype values given among the columns of the smList components of sms

sms

an instance of smlSet

...

additional parameter to plot

Value

• a plot is rendered on the current display

Details

When the genotype is categorical, will use boxplots; when genotype has been imputed and includes expected allele counts, will use a scatterplot.

Examples

if ("GGtools" %in% installed.packages()[,1]) {
  s20 = getSS("GGtools", "20")
  plot_EvG(genesym("CPNE1"), rsid("rs6060535"), s20)
 }