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 [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.