visTrans: Visualize trans-eQTL Results
In GeneticTools: Collection of Genetic Data Analysis Tools

Description Usage Arguments Details Value Author(s) Examples

Plot function for the visualization of trans-eQTL results.

1	visTrans(snpGene, geneAnnot)

`snpGene`	A dataframe indicating the snp-gene association, see details.
`geneAnnot`	An annotation track.

Typically are trans-eQTL difficult to visualize. One possible option is this plot. It takes as an input a dataframe in bed format. This one is typically provided from an eQTL run with set parameter sig in the bed list. The dataframe indicates then all significant associations between genes and SNPs and these associations are then connected within the Figure with arches.

In addition it is possible to plot an annotation track, by specifying it in geneAnnot. This track is required to be in bed format and the column names are Name, Chr, Start and Stop. In case a standard Ensemble gtf file is used for that the function gtfToBed provides the correct input for this option.

A figure.

Daniel Fischer

  # This is just simulated data and hence we cannot see results as with real data. 
  # An example for real data is shown in the vignette and as soon as this data is
  # freely available this example will be updated.
  
  # See also the vignette for a more detailed example.
 
  data(Xgene) 
  data(genotData)
  data(annotTrack)
## Not run: 
  annotBed <- gtfToBed(annotTrack)
  
  lm.myEQTLtrans <- eQTL(gex=Xgene, geno=genotData, xAnnot=annotBed, 
                         method="LM", windowSize=NULL, sig=0.01)

  snpGeneInfo <- lm.myEQTLtrans$bed
# Plot the visualization
  visTrans(snpGene=snpGeneInfo,annotBed)

## End(Not run)