Plot function for the visualization of trans-eQTL results.
A dataframe indicating the snp-gene association, see details.
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
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
In addition it is possible to plot an annotation track, by specifying it in
track is required to be in bed format and the column names are
Stop. In case a standard Ensemble gtf file is used for that the function
provides the correct input for this option.
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# 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)
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