[R] Violin plots in R

Hi All, I need your help in making the violin plot in R using the data which is attached herewith. I am new to R and having issues in tidying my data for R. I am trying the code but I am not able to tidy my data for violin plot in ggplot. Any help will be highly appreciated. Thanks, Puja ___

Re: [R] Need in formatting data for circos plot

ty jsou důvěrné > a podléhají tomuto právně závaznému prohlášení o vyloučení odpovědnosti: > https://www.precheza.cz/01-dovetek/ | This email and any documents > attached > to it may be confidential and are subject to the legally binding > disclaimer: > https://www.precheza.cz/en/01-

[R] Need in formatting data for circos plot

Hi All, I have gene expression data with differential fold change value and the file looks like as below: Chrom start_pos end_pos value 14 20482867 20496901 2.713009346 4 123712710 123718202 -2.20797815 13 80883384 80896042 1.646405782 16 48842551 48844461 -1.636002557 17 28399094 28517527 1.03306

Re: [R] Unable to extract gene list from chromosome

for someone to reply. Thanks, Puja On Thu, Apr 8, 2021 at 7:28 PM David Winsemius wrote: > > On 4/8/21 3:42 PM, pooja sinha wrote: > > Hi David, > > Sorry I forgot to attach the file. Now it's attached. > > > Now when I go back and check the values of the setu

Re: [R] Unable to extract gene list from chromosome

Hi David, Sorry I forgot to attach the file. Now it's attached. Thanks, Puja On Thu, Apr 8, 2021 at 6:01 PM David Winsemius wrote: > > On 4/8/21 2:30 PM, pooja sinha wrote: > > Hi All, > > > > I am trying to extract gene list from chromosome number and posi

[R] Unable to extract gene list from chromosome

Hi All, I am trying to extract gene list from chromosome number and position, for that I am using biomaRt in R but I am getting error messages as shown below. Also below is the code I am using for extraction. library("biomaRt") listMarts() ensembl <- useMart("ensembl") datasets <- listDatasets(en

Re: [R] merging multiple .csv files

(aka Berkeley Breathed in his "Bloom County" comic strip ) > > > On Tue, Dec 15, 2020 at 1:36 PM pooja sinha wrote: > >> Hi All, >> >> I have 10 .csv files containing 12 to 15 columns but have some columns in >> common. I need to join all of

[R] merging multiple .csv files

Hi All, I have 10 .csv files containing 12 to 15 columns but have some columns in common. I need to join all of my .csv files into one using one common column ‘Pos’. The header portion of my .csv files looks as shown below: Chrom Pos Avg Stdev A15_3509.C A31_3799.C A32_3800.C A35_3804.C Gene ID

Re: [R] Unable to resolve the issue of break point in ggplot2

Sorry I used limits in code and need to focus on both limits and breaks. On Wed, Feb 26, 2020 at 9:51 AM pooja sinha wrote: > Hi All, > > I have a data as shown below: > TF YT_YC MT_MC AT_AC > GRHL2 1e-2597 1e-2789 1.00E-281 > Srebp1a 1e-1860 1e-1744 1e-944 > EWS:ERG 1

[R] Unable to resolve the issue of break point in ggplot2

Hi All, I have a data as shown below: TF YT_YC MT_MC AT_AC GRHL2 1e-2597 1e-2789 1.00E-281 Srebp1a 1e-1860 1e-1744 1e-944 EWS:ERG 1e-1831 1e-2127 1e-548 EWS:FLI1 1e-1580 1e-1937 1.00E-166 NFAT 1e-1418 1e-2224 1e-761 Sox4 1e-1410 1e-1839 1.00E-246 PU.1-IRF 1e-1361 1e-3661 1e-1380 Sox2 1e-1114 1e-12

Re: [R] Problems in writing code for circos plot

ould 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 wrote: > > > > Hi All, > > > > I have attached the three different datasets for Rn6 genome (r

Re: [R] Unable to make plots using ggplot2

> #scale_y_continuous(trans = "log10") + >theme(axis.text.x = element_text(angle = 60, vjust = 1)) > > > Hope this helps, > > Rui Barradas > > > Às 22:01 de 16/02/20, pooja sinha escreveu: > > Hi All, > > > > I have data in excel with the

[R] Unable to make plots using ggplot2

Hi All, I have data in excel with the following details: CHG_methylation Young_Control Young_Treated 0-10% 95.23 94.53 10-20% 3.71 4.16 20-30% 0.68 0.8 30-40% 0.18 0.22 40-50% 0.07 0.09 50-60% 0.04 0.06 60-70% 0.02 0.04 70-80% 0.02 0.03 80-90% 0.02 0.03 90-100% 0.04 0.05 I am trying to plot the gr

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.

[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 c

Re: [R] How to extract or sort values from one column

It worked, initially I made some mistake. Thanks a lot. Trying to read basics of R. Puja On Fri, Jan 31, 2020 at 1:06 PM pooja sinha wrote: > Thanks but it gives error "incorrect number of dimensions". > > > Best, > Puja > > On Fri, Jan 31, 2020 at 11:37 AM K

Re: [R] How to extract or sort values from one column

a good idea to start reading some introductory > tutorials. These are basic things you can find in all tutorials :-) > > Best, > Kimmo > > pe, 2020-01-31 kello 10:50 -0500, pooja sinha kirjoitti: > > Thanks for providing the code but I also needed the output sheet in > >

Re: [R] How to extract or sort values from one column

ored in a data frame called 'df'. So this > > code should do the job: > > > > df$Value[ (df$Value>=0.2 & df$Values<=0.4) | df$Value>=0.7 ] > > > > Best, > > Kimmo > > > > > > > > pe, 2020-01-31 kello 09:21 -0500, pooj

[R] How to extract or sort values from one column

Hi All, I have a .csv file with four columns (Chrom, Start_pos, End_pos & Value). The value column range from 0 to 1.0 having more than 2.8 million rows. I need to write a code from which I can extract the values from 0.2-0.4 & 0.7-1.0. Could anyone help me in writing the code because I am new to

[R] Problems in writing code for circos plot

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 ( http

[R] Fwd: Problem in plotting Circos plot with the attached dataset

-- Forwarded message - From: pooja sinha Date: Fri 24 Jan, 2020, 15:06 Subject: Problem in plotting Circos plot with the attached dataset To: YOUNGCONTROL.csv <https://drive.google.com/file/d/1arQqlzkRJybclikAByB9w9TCnvmD_Y46/view?usp=drive_web> YOUNGTREATED.csv

[R] Problem in plotting Circos plot with the attached dataset

YOUNGCONTROL.csv YOUNGTREATED.csv Hi I have attached the three different datasets for Rn6 genome and I needed to use circos