GenomicTools (version 0.2.9.7)

plot.eqtl: Plot an eqtl Object

Description

The function offers informative plots for an eqtl object.

Usage

# S3 method for eqtl
plot(x, file = NULL, which = NULL, sig = 0.01, verbose = TRUE, 
                     centered = TRUE, log = FALSE, mc.cores = 1, genome = NULL, ...)

Arguments

x

Object of class eqtl.

file

Store set of graphics under that file name.

which

Specifies for which genes should the plot be created.

sig

Chosen significance level.

verbose

Logical, extended feedback of the function.

centered

Logical, plot should be centered around center gene.

log

Logical, y-axis scale is log(base=10)-scaled.

mc.cores

Amount of cores for parallel computing.

genome

The name of an existing genome.

...

Additional plotting parameters.

Details

This function plots the test results of an eqtl object. Typically is the tested gene in the center and the p-values of associated SNPs are visualized. Monomorphic SNPs and those that were missing are separately plotted. Test results that are smaller than the value given to sig are marked in red. The y.axis can be switched to log10 scale by setting the logical parameter log=TRUE in that case are bars instead of dots plotted. If the y-axis is on log-scale it is also possible to give a second eqtl object to the function and plot the test results for both.

The annotation feature is currently under development and only available in limited form.

Examples

# NOT RUN {
# Load the data
  data("annotTrack")   
  data("geneEXP")      
  data("genotData") 
# }
# NOT RUN {
# A cis eQTL for 10 different genes:
  EQTL1 <- eQTL(gex=geneEXP[,1:10] , xAnnot = annotTrack,
                geno= genotData)

# A trans-eQTl for two different genes:
  EQTL2   <- eQTL(gex=geneEXP[,c(1,1000)] , xAnnot = annot.bed, 
                  geno= genotData, windowSize = NULL)

# Visualize the second cis-eQTL:
  plot(EQTL1, which=2)
  
# Visualize the trans-eQTL
  plot(EQTL2)
# }