Re: [R] Plotting DMRs (Differentially Methylated Regions) using Gviz package in R
Thanks, I'll check it out.
On Fri, Feb 7, 2020 at 1:08 PM Martin Morgan
wrote:
> 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-boun...@r-project.org on behalf of pjsinh...@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 = "28225",
> chromosome = Chrom$chr1, name = "DMRs")
>
> itrack <- IdeogramTrack(genome = genome, chromosome = chr)
>
> plotTracks(track1, itrack)
>
>
> If anyone know how to plot and correct my code including how to add
> methylation difference values, then that will be of great help.
>
>
> Thanks,
>
> Puja
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
[[alternative HTML version deleted]]
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Re: [R] Plotting DMRs (Differentially Methylated Regions) using Gviz package in R
Probably have more success asking on https://support.bioconductor.org.
Martin Morgan
On 2/7/20, 12:57 PM, "R-help on behalf of pooja sinha"
wrote:
Hi All,
I have a file list consisting of Chromosome, Start , End & Methylation
Difference in the following format in excel:
Chrom Start End Meth. Diff
chr1 38565900 38566000 -0.20276818
chr1 38870400 38870500 -0.342342342
chr1 39469400 39469500 -0.250260552
chr1 52013600 52013700 -0.37797619
chr1 52751700 52751800 0.257575758
chr1 75505100 75505200 -0.262847308
I need help in plotting the DMRs using Gviz package in R. I tried a code
below but it doesn't turn out correct.
library(GenomicRanges)
library(grid)
library(Gviz)
library(rtracklayer)
library(BSgenome)
library(readxl)
library(BSgenome.Rnorvegicus.UCSC.rn6)
genome <- getBSgenome("BSgenome.Rnorvegicus.UCSC.rn6")
genome
data1 <- read_excel("DMRs_plots.xlsx")
head(data1)
data1$Chrom = Chrom$chr1
track1 <- DataTrack(data = data1, from = "38565900" , to = "28225",
chromosome = Chrom$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.
__
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.
[R] Plotting DMRs (Differentially Methylated Regions) using Gviz package in R
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 = "28225",
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.
