[R] Plotting DMRs (Differentially Methylated Regions) using Gviz package in R

[Martin Morgan]

Probably have more success asking on https://support.bioconductor.org.

Martin Morgan

On 2/7/20, 12:57 PM, "R-help on behalf of pooja sinha" <r-help-bounces using r-project.org on behalf of pjsinha07 using gmail.com> wrote:

    Hi All,
    
    I have a file list consisting of Chromosome, Start , End & Methylation
    Difference in the following format in excel:
    
    Chrom     Start          End          Meth. Diff
    
    chr1     38565900 38566000 -0.20276818
    
    chr1     38870400 38870500 -0.342342342
    
    chr1     39469400 39469500 -0.250260552
    
    chr1     52013600 52013700 -0.37797619
    
    chr1     52751700 52751800  0.257575758
    
    chr1     75505100 75505200 -0.262847308
    
    I need help in plotting the DMRs using Gviz package in R. I tried a code
    below but it doesn't turn out correct.
    
    library(GenomicRanges)
    library(grid)
    library(Gviz)
    library(rtracklayer)
    library(BSgenome)
    library(readxl)
    library(BSgenome.Rnorvegicus.UCSC.rn6)
    genome <- getBSgenome("BSgenome.Rnorvegicus.UCSC.rn6")
    genome
    data1 <- read_excel("DMRs_plots.xlsx")
    head(data1)
    data1$Chrom = Chrom$chr1
    
    track1 <- DataTrack(data = data1, from = "38565900" , to = "282250000",
    chromosome = Chrom$chr1, name = "DMRs")
    
    itrack <- IdeogramTrack(genome = genome, chromosome = chr)
    
    plotTracks(track1, itrack)
    
    
    If anyone know how to plot and correct my code including how to add
    methylation difference values, then that will be of great help.
    
    
    Thanks,
    
    Puja
    
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