Re: [R] identify the distribution of the data

possible > distribution > you could use package > > https://cran.r-project.org/web/packages/fitdistrplus/index.html > > Cheers > Petr > > > -Original Message- > > From: R-help On Behalf Of Bogdan Tanasa > > Sent: Wednesday, February 8, 2023 5:35 PM > &g

[R] identify the distribution of the data

Dear all, I do have dataframes with numerical values such as 1,9, 20, 51, 100 etc Which way do you recommend to use in order to identify the type of the distribution of the data (normal, poisson, bernoulli, exponential, log-normal etc ..) Thanks so much, Bogdan [[alternative HTML versi

Re: [R] overlaying two graphs / plots /lines

,lty=2,col="blue") > > legend(150,400,c("A","B"),lty=1:2,col=c("red","blue")) > > > > There are other tricks to deal with the differences in range between A > and B. > > > > Jim > > > > On Wed, Feb 8,

[R] overlaying two graphs / plots /lines

Dear all, Any suggestions on how I could overlay two or more graphs / plots / lines that have different sizes and the x axes have different breakpoints. One dataframe is : A : on x axis : 1 , 7, 9, 20, etc ... (100 elements) on y axis : 39, 91, 100, 3, etc ... (100 elements) The other datafra

Re: [R] confidence intervals

ity. > > > > Tim > > > > *From:* David Winsemius > *Sent:* Thursday, September 8, 2022 8:51 PM > *To:* Bogdan Tanasa > *Cc:* Ebert,Timothy Aaron ; r-help > *Subject:* Re: [R] confidence intervals > > > > *[External Email]* > > The first article ha

Re: [R] confidence intervals

write the correct code. > > You might spend some time looking for a scientific paper that uses that > equation for the confidence interval and thereby get some context to > explain why the equation is correct. > > Tim > > -Original Message- > From: R-help On Beha

Re: [R] confidence intervals

derstand the > principles underlying this resource? > > > -- > > David. > > On 8/26/22 17:55, Bogdan Tanasa wrote: > > Dear all, > > > > Although I know that it is not a statistics mailing list, given my work > on > > ICeChIP > > > > > https:

[R] hdf5 files

Dear all, is there a way to read rge hd5 files in R without using hdf5r library ? Thanks, Bogdan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r

Re: [R] installing an R package

ius wrote: > > Pretty sure the right way to install that package is with the Bioc > installer. > > or simply install.packages() after setting the repository. > > > Best, > Uwe Ligges > > > > > Sent from my iPhone > > > >> On Apr 28, 2022, at 3:35

[R] installing an R package

HI everyone, I must transfer a package from one platform (AWS) where I was able to install the package to another platform (local PC), where I am not able to install the package. The package is called : BSgenome.Hsapiens.UCSC.hg38 Is there a way to transfer the files from BSgenome.Hsapiens.UCSC

Re: [R] help with installing R packages on Mac : these packages are downloaded but not compiled

n't know whether this is Mac specific or not. Folks on the > >Mac list presumably would). > > > > > >Bert Gunter > > > >"The trouble with having an open mind is that people keep coming along > >and sticking things into it." > >-- Opus (

[R] arrow keys in R

In R, I do press the arrow keys, and 2 things happen : On one hand, the symbols ^[[A^[[A^[[A appear; On the other hand, shall I start typing a command, such as "library", I begin by typing the first 2 letters "li", click "left arrow", and the result is "li "(i.e. lots of spaces) instead of having

[R] Error in loadNamespace(i, c(lib.loc, .libPaths())

Dear all, i am using Monocle3 in order to study disease development by single-cell technologies : https://cole-trapnell-lab.github.io/monocle3/ When I am installing additional packages like "spData" from https://nowosad.github.io/spData/, I am getting the message : Error in loadNamespace(i, c

[R] extracting a R object from an R image

Dear all, I saved my work in a Rimage that contains multiple objects ; the objects were generated with Monocle3 : https://cole-trapnell-lab.github.io/monocle3/docs/starting/ one object is called CDS. How shall I extract this object CDS (that has a complex structure) from the R image ? thank y

[R] docker containers and R

Dear all, would you please advise : shall I have a container that runs R (below), and install specifically a package called UMI4Cats, obviously, a lot of other libraries are installed.How can I save the docker container that contains the additional libraries that I have installed and are required

[R] R code in RData

Dear all, would you please advice : I have an Rdata file, what is the way to print the R code that has been used inside the Rdata file ? thank you, Bogdan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSC

Re: [R] about a p-value < 2.2e-16

aper, then go ahead and do it. > > Best, > Jiefei > > > > Bogdan Tanasa 于 2021年3月20日周六 上午2:39写道： > >> Thank you Kevin, their wording is "Please note that the exact p value >> should be provided, when possible, etc" >> >> by "exact p-va

Re: [R] about a p-value < 2.2e-16

Shing Knowledge Institute of St. Michael's > Assistant Professor, Dalla Lana School of Public Health > University of Toronto > email: kevin.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 > > > On Mar 19, 2021, at 1:22 PM, Bogdan Tanasa wrote: > > > > EX

Re: [R] about a p-value < 2.2e-16

>Spencer >> > > >> > > Best, >> > > Jiefei >> > > >> > > >> > > >> > > On Fri, Mar 19, 2021 at 10:01 PM Jiefei Wang >> wrote: >> > > >> > >> Hey, >> > >> >>

Re: [R] about a p-value < 2.2e-16

s Bogdan asked in his first email, >> or it could mean the p-value calculated from the exact distribution of the >> statistic(In this case, U stat). These two are actually not related, even >> though they all called "exact". >> >> Best, >> Jiefei &

Re: [R] about a p-value < 2.2e-16

re: > > https://stat.ethz.ch/R-manual/R-devel/library/stats/html/wilcox.test.html > > Hope this helps! > > Best, > > VD > > > On Thu, Mar 18, 2021 at 10:36 PM Bogdan Tanasa wrote: > >> Dear Peter, thanks a lot. yes, we can see a very precise p-value,

Re: [R] about a p-value < 2.2e-16

; > hold, and all models are wrong (but some are useful), as George Box > > famously said years ago.[1] Truth only exists in mathematics, and > > that's because it's a fiction to start with ;-) > > > > > >Hope this helps. > >Spencer G

Re: [R] about a p-value < 2.2e-16

such thing > as an "exact p value" except to the extent that certain assumptions > hold, and all models are wrong (but some are useful), as George Box > famously said years ago.[1] Truth only exists in mathematics, and > that's because it's a fiction to start wit

[R] about a p-value < 2.2e-16

Dear all, i would appreciate having your advice on the following please : in R, the wilcox.test() provides "a p-value < 2.2e-16", when we compare sets of 1000 genes expression (in the genomics field). however, the journal

Re: [R] overlaying frequency histograms or density plots in R

= ..density..), >position = position_dodge(), >bins = 10) > > p + geom_histogram( >mapping = aes(y = ..density..), > position = position_dodge(), >bins = 10) + >scale_y_continuous(labels = scales::label_percent()) > > > Hope this helps, > >

Re: [R] overlaying frequency histograms or density plots in R

p+geom_histogram(position="dodge") > > Cheers > Petr > > -Original Message- > > From: R-help On Behalf Of Bogdan Tanasa > > Sent: Wednesday, February 24, 2021 11:07 PM > > To: r-help > > Subject: [R] overlaying frequency histograms or de

[R] overlaying frequency histograms or density plots in R

Dear all, we do have a dataframe with a FACTOR called EXP that has 3 LEVELS ; head(pp_ALL) VALUE EXP 1 1639742 DMSO 2 1636822 DMSO 3 1634202 DMSO shall i aim to overlay the relative frequency histograms, or the density histograms for the FACTOR LEVELS, please would you let me know why the

Re: [R] algorithms that cluster time series data

> look for R packages that perform the relevant analyses. > > Sarah > > On Mon, Jul 6, 2020 at 1:11 PM Bogdan Tanasa wrote: > > > > Dear all, > > > > please may I ask for a suggestion regarding the algorithms to cluster the > > expression data in single ce

[R] algorithms that cluster time series data

Dear all, please may I ask for a suggestion regarding the algorithms to cluster the expression data in single cells (scRNA-seq) at multiple time points : we do have expression data for 30 000 genes in 10 datasets that have been collected at multiple time points, and i was wondering if you could

Re: [R] 2 docker containers with R ?

thanks a lot, Ashim, and Ivan ! On Sat, Apr 11, 2020 at 4:25 AM Ashim Kapoor wrote: > Dear Bogdan, > > Perhaps > > https://rstudio.github.io/packrat/ > > can be of help? > > Best, > Ashim > > On Sat, Apr 11, 2020 at 4:47 PM Ivan Krylov wrote: > >>

[R] 2 docker containers with R ?

Dear all, we wish everyone a safe and healthy time ! i'm looking forward to have you suggestions please : I am using a R package that is called Seurat for scRNA-seq analysis (https://satijalab.org/seurat/) that has two versions (version 2 or version3 with distinct functions); i'd appreciate if y

[R] a package with randomization/permutation tests for genomic analyses

Dear all, please would you let me know, is there a package in R that has implemented randomization/permutation tests for joint genomic analyses (an example of joint genomic analyses -- when jointly considering both GENE EXPRESSION and PROTEIN BINDING along the DNA). The context of my question is

Re: [R] about .function

appreciate it ! thank you Duncan ! On Thu, Jan 30, 2020 at 11:18 AM Duncan Murdoch wrote: > On 30/01/2020 1:38 p.m., Bogdan Tanasa wrote: > > Dear all, > > > > if I may ask please a very simple question : > > > > what does "." mean in front of funct

[R] about .function

Dear all, if I may ask please a very simple question : what does "." mean in front of function name : an example below . thank you very much ! .set_pbmc_color_11<-function() { myColors <- c( "dodgerblue2", "green4", "#6A3D9A", # purple "grey"

[R] about paired or unpaired t.test or wilcox.test in R

Dear all, if would be great if you could please advise on the use of PAIRED or UNPAIRED T.TEST or WILCOX.TEST in R : let's say shall we have 2 samples : -- CONTROL : where we measure the expression of 100 genes G1 ... G100 in one million cells C1 ...C1mil -- TREATMENT : where we measure the exp

Re: [R] computing standard deviation in R and in Python

3, byrow=T) > > apply(z, 1, sd1) # R > apply(z, 1, sd2) # Python > > apply(z, 2, sd1) # R > apply(z, 2, sd2) # Python > > > Hope this helps, > > Rui Barradas > > Às 11:27 de 24/05/19, Bogdan Tanasa escreveu: > > Dear all, please would you advise : > &

[R] computing standard deviation in R and in Python

Dear all, please would you advise : do python and R have different ways to compute the standard deviation (sd) ? for example, in python, starting with : a = np.array([[1,2,3], [4,5,6], [7,8,9]]) print(a.std(axis=1)) ### per row : [0.81649658 0.81649658 0.81649658] print(a.std(axis=0)) ### per c

Re: [R] to run an older version of R on my machine

ntu. I would advise you to try it anyhow. Good luck with that! > > All the best, > > Alfredo > > El jue., 23 may. 2019 a las 21:38, Bogdan Tanasa () > escribió: > >> Dear all, >> >> if you could help me please with a solution to a simple question : >> &g

[R] to run an older version of R on my machine

Dear all, if you could help me please with a solution to a simple question : i believe that my ubuntu machine automatically installed R 3.6.0 : when i type : > R. it says : R version 3.6.0 (2019-04-26) -- "Planting of a Tree" Copyright (C) 2019 The R Foundation for Statistical Computing Platform

[R] display of ECDF

Dear all, please could you advise me on the following : I would like to display a few CDF data (the R code is below), by using a set of numerical BREAKS on a X axis to be shown at EQUAL DISTANCE from each other (although numerically, the BREAKS are on log10 axis and do not reflecting an equal dist

Re: [R] selecting the COLUMNS in a dataframe function of the numerical values in a ROW

zgene[2,1:4] > 0] > TTT TTA > gene1 0 0 > gene2 1 1 > gene3 0 1 > gene4 0 0 > > > > zgene[ , zgene[rownames(zgene) == "gene2",1:4] > 0] > TTT TTA > gene1 0 0 > gene2 1 1 > gene3 0 1 > gene4 0 0 >

Re: [R] selecting the COLUMNS in a dataframe function of the numerical values in a ROW

gene4 > > > > ygene <- data.frame(TTT=c(0,1,0,0), > + TTA=c(0,1,1,0), > + AGA=c(0,0,0,0), > + gene=c("gene1", "gene2", "gene3", "gene4")) > > > > ygene[ , colSums(ygene[,1:3])

[R] selecting the COLUMNS in a dataframe function of the numerical values in a ROW

Dear all, please may I ask for a suggestion : considering a dataframe that contains the numerical values for gene expression, for example : x = data.frame(TTT=c(0,1,0,0), TTA=c(0,1,1,0), ATA=c(1,0,0,0), gene=c("gene1", "gene2", "gene3", "gene4")) ho

[R] about the series of numbers

Dear all, if I may ask please a question that is likely very naive : shall I write in R > "1:9", it will generate "1 2 3 4 5 6 7 8 9" shall I write > "0.1:0.9", why does it generate only 0.1 ? thank you ! -- bogdan [[alternative HTML version deleted]]

Re: [R] installing R 3.5.1

25, 2018 at 8:02 AM, Berwin A Turlach wrote: > Dear Bogdan, > > On Sat, 25 Aug 2018 07:24:40 -0700 > Bogdan Tanasa wrote: > > > installed E: Unable to correct problems, you have held broken > > packages. > > Perhaps this is the problem, did you try "

[R] installing R 3.5.1

Dear Benoit, many thanks for your suggestions. Have a good weekend ! Message: 26 Date: Sat, 25 Aug 2018 11:13:49 +0200 From: Benoit Vaillant To: Bogdan Tanasa Cc: r-help Subject: Re: [R] installing R 3.5.1 Message-ID: <20180825091348.7tidm7fvhiudr...@auroras.fr> Content-Type: text

Re: [R] installing R 3.5.1

ell installed .. On Sat, Aug 25, 2018 at 12:51 AM Berwin A Turlach wrote: > G'day Bogdan, > > On Fri, 24 Aug 2018 18:28:59 -0700 > Bogdan Tanasa wrote: > > > I am trying to install R 3.5.1 on my Ubuntu 14.04 system; however, I > > am getting the following

[R] installing R 3.5.1

Dear all, I am trying to install R 3.5.1 on my Ubuntu 14.04 system; however, I am getting the following message : sudo apt-get install r-base [...] The following packages have unmet dependencies: r-base : Depends: r-recommended (= 3.5.1-1trusty) but it is not going to be installed E: Unable to c

Re: [R] a suggestion about the display of structural variants in R

ey are typically found on the Bioconductor > mailing list, not this list. > > On Sat, 28 Jul 2018, Bogdan Tanasa wrote: > > Dear Boris, >> >> good morning, and thank you for your message. After thinking a bit more >> yesterday, I believe that I could adapt the functiona

Re: [R] a suggestion about the display of structural variants in R

ignettes/ > OmicCircos/inst/doc/OmicCircos_vignette.pdf) > > However the Bioconductor Project has its own support mailing list, R-Help > is for programming help. > > > B. > > > > > On 2018-07-28, at 02:24, Bogdan Tanasa wrote: > > > > Dear all, >

[R] a suggestion about the display of structural variants in R

Dear all, we wish you a fruitful and refreshing weekend ! Thought that I may also write to ask you for a suggestion, specifically if you could please advise on whether there is any package already built (in R) that could help with the following data visualization : we have a set of mutations

Re: [R] initiate elements in a dataframe with lists

gt; 1 DEL chr1 10 chr1 30 chr1 > 2 DEL chr1 15 chr1 100 chr1 > 3 DUP chr1 120 chr1 300 chr1 > 4 TRA chr1 340 chr2 20 > 5 INV chr2 100 chr2 200 > 6 TRA chr2 220 chr1 320 chr1 > > Note that depending on what you pla

Re: [R] initiate elements in a dataframe with lists

an after the experiment is done may be no more > than asking him to perform a post-mortem examination: he may be able to say > what the experiment died of. ~ Sir Ronald Aylmer Fisher > The plural of anecdote is not data. ~ Roger Brinner > The combination of some data and an aching desire f

Re: [R] initiate elements in a dataframe with lists

> >> >> /// >> To call in the statistician after the experiment is done may be no more >> than asking him to perform a post-mortem examination: he may be able to say >> what th

Re: [R] initiate elements in a dataframe with lists

Thank you Juan. On Wed, Jul 25, 2018 at 12:56 AM, Juan Telleria Ruiz de Aguirre < jtelleria.rproj...@gmail.com> wrote: > Check tidyverse's purrr package: > > https://github.com/rstudio/cheatsheets/raw/master/purrr.pdf > > In the second page of the cheatsheet there is info on how to create list >

[R] initiate elements in a dataframe with lists

Dear all, assuming that I do have a dataframe like : x <- data.frame(TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA"), CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2"), POSA=c(10, 15, 120, 340, 100, 220), CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1"), POSB=c(30, 100, 300, 20, 200,

Re: [R] coloring edges in IGRAPH

Thank you all. Think I did solve it by using the code below : plot(g_decompose[[1]], edge.color=edge_attr(g_decompose[[1]])$COLOR) plot(g_decompose[[2]], edge.color=edge_attr(g_decompose[[2]])$COLOR) On Tue, Jul 24, 2018 at 5:48 PM, Bogdan Tanasa wrote: > Dear all, > > I would app

[R] coloring edges in IGRAPH

Dear all, I would appreciate a piece of advice please : I am aiming to color the edges in a graph, by using IGRAPH package. It works well for the big braph, however, when I decompose the graph into 2 subgraphs and color code those, the color of the edges change (unexpectedly). more precisely, as

Re: [R] help with merging two dataframes function of "egrep"-like formulas

1 a*b::x*y > > #' Created on 2018-07-18 by the [reprex package](http://reprex.tidyver > se.org) (v0.2.0). > #### > > Note that this is preferable if you can avoid ever creating the complex > data z in B, but Bx is much more flexible and less error prone than B

Re: [R] help with merging two dataframes function of "egrep"-like formulas

t;> "a*b" of A with the row with "a*b::x*y" of B. > > > This may be what you are looking for: > > library(fuzzyjoin) > > The inner join returns just the one row where the string matches. > B %>% > regex_inner_join(A, by = c(z = 'z')

Re: [R] help with merging two dataframes function of "egrep"-like formulas

) > > The inner join returns just the one row where the string matches. > B %>% > regex_inner_join(A, by = c(z = 'z')) > > While the full join returns NA's where the string does not match. > B %>% > regex_full_join(A, by = c(z = 'z')) > &g

[R] help with merging two dataframes function of "egrep"-like formulas

Dear all, please may I ask for a piece of advise regarding merging two dataframes : A <- data.frame(z=c("a*b", "c*d", "d*e", "e*f"), t =c(1, 2, 3, 4)) B <- data.frame(z=c("a*b::x*y", "c", "", "g*h"), t =c(1, 2, 3, 4)) function of the criteria : if "the elements in the 1st column of A could be

Re: [R] even display of unevenly spaced numbers on x/y coordinates

, Jeff Newmiller wrote: > But did you run the code? Apparently not. > > On July 14, 2018 10:34:32 PM PDT, Bogdan Tanasa wrote: > >Dear Jeff, > > > >thank you for your prompt reply and kind help. > > > >During our previous conversation, we worked on a differ

Re: [R] even display of unevenly spaced numbers on x/y coordinates

). Thanks again, and happy weekend ;) ! -- bogdan On Sat, Jul 14, 2018 at 10:25 PM, Jeff Newmiller wrote: > Isn't this what I showed you how to do in [1]? > > [1] https://stat.ethz.ch/pipermail/r-help/2018-July/455215.html > > On July 14, 2018 10:16:36 PM PDT, Bogdan Tanasa

[R] even display of unevenly spaced numbers on x/y coordinates

Dear all, please would you advise on how I could make an even display of unevenly spaced number on a graph in R. For example, considering the code below : BREAKS = c(0, 0.1, 1, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500) a <- seq(0,100,0.1) b <- seq(0,1000,0.1) plot(ecdf(a), co

Re: [R] about ECDF display in ggplot2

legend.box = "horizontal", > legend.key.size = unit(1, "cm"), > axis.title = element_text(size = 12), > legend.text = element_text(size = 9), > legend.title=element_text(face = "bold", size = 9)) > > #' ![](f

Re: [R] about ECDF display in ggplot2

ze = 9)) > > dev.off() On Sat, Jul 7, 2018 at 9:47 PM, Jeff Newmiller wrote: > It is a feature of ggplot that points excluded by limits raise warnings, > while base graphics do not. > > You may find that using coord_cartesian with the xlim=c(0,500) argument > works be

[R] about ECDF display in ggplot2

Dear all, I would appreciate having your advice/suggestions/comments on the following : 1 -- starting from a vector that contains LENGTHS (numerically, the values are from 1 to 10 000) 2 -- shall I display the ECDF by using the R code and some "limits" : BREAKS = c(0, 10, 20, 30, 40, 50, 60, 70

[R] a question about R script : "Can only modify plain character vectors."

Dear all, would appreciate a suggestion about the following situation : I am running a script in R, and shall i execute it in the terminal, step by step, it works fine. however, if i do source ("script.R"), it does not complete and I am getting the error : "Can only modify plain character vector

[R] splitting a dataframe in R based on multiple gene names in a specific column

I would appreciate please a suggestion on how to do the following : i'm working with a dataframe in R that contains in a specific column multiple gene names, eg : > df.sample.gene[15:20,2:8] Chr Start End Ref Alt Func.refGene Gene.refGene284 chr2 16080996 16080996 C T ncRNA_e

Re: [R] submitting R scripts with command_line_arguments to PBS HPC clusters

ler" would be the kind of action that would > run R with very different environment variables and possibly different > access credentials than your usual interactive terminal. A thorough > reading of the "Installation and Administration Guide" and some study of > your HP

[R] submitting R scripts with command_line_arguments to PBS HPC clusters

Dear all, please could you advise me on the following : I've written a R script that reads 3 arguments from the command line, i.e. : " args <- commandArgs(TRUE) TUMOR <- args[1] GERMLINE <- args[2] CHR <- args[3] ". when I submit the R script to a PBS HPC scheduler, I do the following (below), b

Re: [R] reshaping the data

gt; > dcast(test, Sample~Gene, fun=function(x) sum(as.numeric(x))) > > 1 means INDEL, 2 means SNV and three means both > > Cheers > Petr > > > > -Original Message- > > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Bogdan > > T

[R] reshaping the data

Dear all, I would appreciate please a piece of help regarding the use of acast/dcast functions in reshape2 package. Specifically, I'm working with a data frame, that has information about SAMPLE, GENE, and TYPE of MUTATION (as shown below): SampleGene Type 22M AEBP1 SNV 17M AE

Re: [R] integrating 2 lists and a data frame in R

gt; Cheers, > Bert > > > 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 Tue, Jun 6, 2017 at 7

Re: [R] integrating 2 lists and a data frame in R

;n1","n2","n3", "n3", "n4"), m=c("m1","m1","m3", > "m4", "m5"), I=c(100,300,400, NA, 0)) > > C >n m I > 1 n1 m1 100 > 2 n2 m1 300 > 3 n3 m3 400 > 4 n3 m4 NA > 5 n4 m

Re: [R] integrating 2 lists and a data frame in R

- - - - > # m3 - - 400 - > # m4 - - - - > # m5 - - - - > > class(MN) > # [1] "xtabs" "table" > # MN is a table. If you want a data.frame > MN <- as.data.frame.matrix(MN) > class(MN) > # [1] "data.frame" > > -

Re: [R] integrating 2 lists and a data frame in R

;m5")) > C <- data.frame(n=c("n1","n2","n3"), m=c("m1","m1","m3"), > I=c(100,300,400)) > MN<-as.data.frame(matrix(NA,nrow=length(N[,1]),ncol=length(M[,1]))) > names(MN)<-M[,1] > rownames(MN)<-N[,1] > C[,1]&l

Re: [R] integrating 2 lists and a data frame in R

Bert Gunter wrote: > Reproducible example, please. -- In particular, what exactly does C look > ilike? > > (You should know this by now). > > -- Bert > Bert Gunter > > "The trouble with having an open mind is that people keep coming along > and sticking things

[R] integrating 2 lists and a data frame in R

Dear all, please could you advise on the R code I could use in order to do the following operation : a. -- I have 2 lists of "genome coordinates" : a list is composed by numbers that represent genome coordinates; let's say list N : n1 n2 n3 n4 and a list M: m1 m2 m3 m4 m5 2 -- and a

Re: [R] about Rstudio

u follow the instructions at https://cran.r-project.org/ > bin/linux/ubuntu/README.html? > -- > Sent from my phone. Please excuse my brevity. > > On May 29, 2017 2:07:27 PM PDT, Bogdan Tanasa wrote: > >Hi Bert, thank you for your email. yes, of course, i did the google > &g

Re: [R] about Rstudio

ime for you to do some homework... > > -- Bert > > > 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 ) > > >

[R] about Rstudio

Dear all, please could you help with an advice : I have installed Rstudio on my Ubuntu PC, and when I initiate the application, it says : "R lib path(/usr/local/lib/R/lib) not found" on my computer, at the path "/usr/local/lib/R/lib" there are the folders : bin etc site-library R is installed

[R] using "dcast" function ?

Dear all, I would like to double-check with you please the use of "acast" or "dcast" function from "reshape2"package. I am starting with a data frame Y of GENES and SAMPLES,eg : Cancer_Gene Sample 1ABL2 WT_10T 2ABL2 WT_6T 3 ADGRA2 HB_8R 4AFF4 EWS_13R and I

Re: [R] differential use of R version

value = NULL) : replacement has length zero On Wed, Apr 5, 2017 at 2:52 AM, Rui Barradas wrote: > Hello, > > Unless you have strong reasons why not, use the most recent one, R 3.3. > > Hope this helps, > > Rui barradas > > > Em 05-04-2017 03:47, Bogdan Tanasa escreveu: >

[R] differential use of R version

Dear all, please could you advise me on the following : on a server, in a folder "x86_64-redhat-linux-gnu-library", i have 2 versions of R (below), with the corresponding BioC libraries : > 3.2 > 3.3 how could i preferentially use an R version or the other (with the related BioC libraries) ? t

[R] tutorials on bootstrap, jackknife, permutation, randomization tests

Dear all, please could anyone recommend a good website/resource describing tutorials on bootstrap, jackknife, permutation, and randomization tests in R, with applications to biology (molecular biology). thanks, -- bogdan [[alternative HTML version deleted]] _

Re: [R] comparing 2 long lists in R

ode you used, and some clear idea of > > what output you expect, it's impossible to figure out how to help you. > > Here are some suggestions for creating a good reproducible example: > > > http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example > >

[R] comparing 2 long lists in R

Dear all, please could you advise on a computationally quick way to compare and merge 2 long lists in R; the lists are of the following type, for example : <> in list 1 : chromosome, coordinateA, coordinateB, value1 chromosome, coordinateC, coordinateC, value2, etc <> in list 2 : chromosome, c

Re: [R] scaling loess curves

et<-„b“ > > > > complete <- rbind(a,b) > > > > p <-ggplot(complete, aes(x=distance, y=intensity, colour=set)) > > p+geom_smooth(method = "loess", size = 1, > span=0.01)+xlab("distance")+ylab("intensity") > > shall do it. > &g

Re: [R] scaling loess curves

i > > > > based on your data maybe using logarithmic y scale shall give you desired > result. > > > > > http://stackoverflow.com/questions/4699493/transform-only-one-axis-to-log10-scale-with-ggplot2 > > > > Or you can recalculate intensity to scale 100-0 (or

Re: [R] scaling loess curves

experiment2 to my email. Shall you have any suggestions, please let me know. Thanks a lot, -- bogdan On Mon, Sep 7, 2015 at 7:34 AM, PIKAL Petr wrote: > Hi > > what about xlim or ylim? > > Cheers > Petr > > > > -Original Message- > > From: R-help [m

[R] scaling loess curves

Dear all, please could you advise about a method to scale 2 plots of LOESS curves. More specifically, we do have 2 sets of 5C data, and the loess plots reflect the relationship between INTENSITY and DISTANCE (please see the R code below). I am looking for a method/formula to scale these 2 LOESS p

Re: [R] reading files with name columns and row columns

read.table(text=txt, head=TRUE, row.names=1) > # X50. X100. > #A5 8 > #B 1314 > read.table(text=txt, head=TRUE, row.names=1, check.names=FALSE) > # 50% 100% > #A 5 8 > #B 13 14 > > > Bill Dunlap > TIBCO Software > wdunlap

Re: [R] reading files with name columns and row columns

your question can be found in > > ?make.names > > for what constitutes a syntactically valid name in R. > > > Cheers, > Bert > > Bert Gunter > > "Data is not information. Information is not knowledge. And knowledge > is certainly not wisdom." >

[R] reading files with name columns and row columns

Dear all, would appreciate a piece of help with a simple question: I am reading in R a file that is formatted as a matrix (an example is shown below, although it is more complex, a matrix of 1000 * 1000 ): the names of the columns are 0, 1, 4, 8, etc the names of the rows are 0, 1

Re: [R] sorting a dataframe

inly not wisdom." >-- Clifford Stoll > > > On Sat, Jun 20, 2015 at 6:29 PM, Diego Miro wrote: > > Bogdan, > > > > Follow my suggestion. > > > > letter <- substring(A, 1, 1) > > number <- substring(A, 2, nchar(A)) > > new.data <

Re: [R] sorting a dataframe

thank you all, it is working fine. happy weekend ;) ! On Sat, Jun 20, 2015 at 6:15 PM, David Winsemius wrote: > > On Jun 20, 2015, at 5:18 PM, Bogdan Tanasa wrote: > > > Dear all, > > > > I am looking for a suggestion please regarding sorting a dataframe with &g

[R] sorting a dataframe

Dear all, I am looking for a suggestion please regarding sorting a dataframe with alphanumerical components : let's assume we have : A = c("A1","A10","A11","A2") B = c(1,2,3,4) C = data.frame(A,B) how could I sort C data.frame in such a way that we have at the end : C$A in the order : "A1", "

Re: [R] display a matrix in colors

Thanks, David, for your time. I found some good tutorials on heatmap.2 and it works : https://www.packtpub.com/books/content/creating-your-first-heat-map-r On Fri, Jun 12, 2015 at 9:12 PM, David Winsemius wrote: > > On Jun 12, 2015, at 5:39 PM, Bogdan Tanasa wrote: > > > Hi Dav

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