Hello,
I've used the Gviz User Guide to create a figure displaying a chromosome ideogram, the coordinate axis, a model of a single gene, and data points indicating the number of variants reported at each nucleotide position. After I successfully created it, I realized that there were data points showing up in the dead center of each intron of the gene model that I did not supply to DataTrack.
This is my code:
lim <- c(117117000, 117311000)
coords <- append(numvars.sort$V2, 117308178)
itrack <- IdeogramTrack(genome="hg19", chromosome="chr7")
gtrack <- GenomeAxisTrack(littleTicks=TRUE)
biomTrack <- BiomartGeneRegionTrack(genome="hg19", chromosome="chr7", start=117119000, end=117309000, name="CFTR", strand="+", stacking="dense")
dtrack <- DataTrack(data=numvars.sort$V3, start = coords[-length(coords)], end = coords[-1], chromosome="chr7", genome="hg19", name = "Number of Variants")
plotTracks(list(itrack, gtrack, biomTrack, dtrack), from=lim[1], to=lim[2])numvars.sort$V2 is a vector of coordinates that matches up to numvars.sort$V3, a vector of the number of variants at each coordinate (ie 1 through 4). I've spot checked multiple places where I see a data point of number of variants = 1 at the center of an intron and they are not in my original supplied vectors. Additionally, I only see these spurious data points when I'm zoomed out sufficiently. If I try to zoom within 100 bp of the spurious data point, it disappears. I'm sorry if this is a weird question but I'm out of ideas of what that problem may be and I've looked over my data many times.
The image I created to show what I mean: graphic
Thank you in advance for your help!
Melissa Lee
PhD candidate
Johns Hopkins School of Medicine
melissa.lee@jhmi.edu
