Gviz package for plotting DMRs
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@ayeshatariq78-22817
Last seen 15 months ago

Hi, I am using Gviz package for plotting DMRs. So far I have successfully created attrack, itrack and Genome axis tracks. I want to create a gtrack with gene annotation information. I have used the following code grtrack <- GeneRegionTrack(DMRs, genome = "hg19", chromosome = chr, name = "Genes", transcriptAnnotation = "symbol", background.title = "brown") plotTracks(list(itrack, gtrack, atrack, grtrack))

The working DMRs file is a Grange object which I have created from a CSV. My original CSV has following information id Chromosome Start End symbol mean.mean.diff ENSG00000272438 chr1 840214 851356 TNFRSF4 -0.036783899

Executing the above I am getting the plot but instead of gene symbol every gene is named as unknown. Can anyone help with that?

Gviz DMRs • 192 views
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Robert Ivanek ▴ 700
@robert-ivanek-5892
Last seen 8 days ago
Switzerland

Hi, As you did not provided complete reproducible example code it is hard for me to help you. When executing the code below I get plot gene with corresponding symbol.

library(Gviz)
DMRs <- read.table(text="id Chromosome Start End symbol mean.mean.diff
ENSG00000272438 chr1 840214 851356 TNFRSF4 -0.036783899",
                   sep=" ", header=T)
DMRs <- as(DMRs, "GRanges")
grtrack <- GeneRegionTrack(DMRs, genome = "hg19", chromosome = "chr1", name = "Genes",
                           transcriptAnnotation = "symbol", background.title = "brown")
plotTracks(grtrack)

Best, Robert

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