Wrong list -- (for which statistical methods question are generally offtopic anyway).
Post here instead: https://www.bioconductor.org/help/ Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Mon, Feb 17, 2020 at 6:58 AM pooja sinha <pjsinh...@gmail.com> wrote: > Hi All, > > > I had previously mentioned that I have large data set with methylation > values ranging from 0-1. The data contains around 3 million rows of values > corresponding to the chromosomal locations. I want to split/sort my data > for plot using circos plot. I thought of doing like sorting the value range > 0.2-0.4 as hypomethylation category and range 0.7-1.0 as hypermethylation > category. However, with this approach the plot again looks cluttered. > Another way is that I can split the data into two parts, one part with > values lower than median, and another part with values larger than median. > > Can anyone suggest me which approach is better or if there are other > approaches I can use in my datasets for circos plot using circlize package. > > > Thanks, > > Puja > > On Sun, Jan 26, 2020 at 5:06 PM Jim Lemon <drjimle...@gmail.com> wrote: > > > Hi Puja, > > Three things: > > 1) Your data files are very large. If you do manage to get circular > > plots out of them with the circlize library they will probably be very > > dense. > > 2) The structure of your data includes too many levels in "Chrom" to > > get the circlize functions to work. I had to pare them back to the > > non-random levels. > > 3) You should probably change the subject line of your message to > > "Would anyone care to do my work for me?" > > > > Jim > > > > On Mon, Jan 27, 2020 at 6:47 AM pooja sinha <pjsinh...@gmail.com> wrote: > > > > > > Hi All, > > > > > > I have attached the three different datasets for Rn6 genome (rat) and I > > > needed to use circos plot by *circlize package in R*. Please anyone > help > > me > > > in writing the code and making the plot. Any help will be highly > > > appreciated. > > > The three file links are below: > > > > > > File 1: YOUNGCONTROL.csv ( > > > https://drive.google.com/open?id=1arQqlzkRJybclikAByB9w9TCnvmD_Y46 ) > > > File 2: YOUNGTREATED.csv ( > > > https://drive.google.com/open?id=1vMidiGmoK4zsYjvf2sT9RbjwF72W0IhO ) > > > File 3: YOUNGTREATED.vs.YOUNGCONTROL.sig.csv ( > > > > > > https://drive.google.com/open?id=0B33BGsdd5x_dOGF0X3BuaWRoMmdSYklOZnJoX09uaWdnNEdN > > > ) > > > > > > The circos plot having the outermost ring contain Rn6 ideogram followed > > by > > > YOUNGCONTROL, YOUNGTREATED & last innermost circle will be of > > > YOUNGTREATED.vs.YOUNGCONTROL.sig > > > > > > 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]] > > ______________________________________________ > 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]] ______________________________________________ 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.
