[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] 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

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

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

[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] 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

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

[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] 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

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

[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] 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] 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] 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 >

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

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

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

[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

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] 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

[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

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 ) > > >

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

[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] 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

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

- - - - > # 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

;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

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

[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] 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] 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] 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] 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

[R] about transforming a data.frame

Dear all, I would appreciate a suggestion on the following : I am working with a data.frame (below) : EXPCT row_names col_names 1 test -5B4:B5:B6B1:B2:B3 2 test -2B7:B8:B9B1:B2:B3 3 test -2D4:D5:D6H4:H5:H6 4 test -2D10:D11:D12 F10:F11:F12 5 test -2

Re: [R] about transforming a data.frame

> for the sample data you provided? > > What code have you tried? I would think table() might be involved, and > possibly strsplit(), but will refrain from putting more time into this > until you provide a reproducible dataset with dput() and some clearer > idea of your intent. >

Re: [R] about transforming a data.frame

lumn), or "D10:D11:D12" > > associate with "2" (in the CT column). > > > > thank you very much, > > > > bogdan > > > > > > > > > > On Fri, May 29, 2015 at 1:32 PM, Sarah Goslee > > wrote: > > > >> Hi, &

Re: [R] about transforming a data.frame

t;"B1:B2:B3" associate with "5, 2, 4" (in CT column), or "D10:D11:D12" > >> associate with "2" (in the CT column). > >> > >> thank you very much, > >> > >> bogdan > >> > >> > >> > >> &

Re: [R] about transforming a data.frame

1:F12 G7:G8:G9 H1:H2:H3 H4:H5:H6 > 210 1111 > 411 0000 > 510 000 0 > > > > On Fri, May 29, 2015 at 4:58 PM, Bogdan Tanasa wrote:

Re: [R] about transforming a data.frame

thanks a lot Sarah, very much appreciate it ! On Fri, May 29, 2015 at 3:18 PM, Sarah Goslee wrote: > LMGTFY: > http://stackoverflow.com/questions/11433432/importing-multiple-csv-files-into-r > > On Fri, May 29, 2015 at 5:58 PM, Bogdan Tanasa wrote: > > Dear Sarah, > >

Re: [R] about transforming a data.frame

Thanks a lot Jim. If I may ask one more little question please, shall I ask the question ""How can I verify that "B1:B2:B3" is paired with ALL of the values 2, 4 and 5 ", regardless of the pairing value (in our case, for the code below, the "pairing value" for "B1:B2:B3" is 1, but it can be 2,3,4

Re: [R] about transforming a data.frame

Hi Jim, thanks again. now I see : the answer to my previous question seems to be yes, as "all" functions works on logical vectors ... best wishes, -- bogdan On Fri, May 29, 2015 at 4:29 PM, Bogdan Tanasa wrote: > Thanks a lot Jim. If I may ask one more little question please, &g

[R] subsetting a dataframe

Dear all, would appreciate your suggestions on subsetting a dataframe : please let's consider an example dataframe df: dd<-c(1,2,3) rows<-c("A1","A2","A3") columns<-c("B1","B2","B3") numbers <- c(400, 500, 600) df <- dataframe(dd,rows,columns, numbers) and a vector : test_rows <-c("A1","A3") ;

[R] accessing the ellements in an array and factors.

Dear all, please could you please with a simple question : I do have an array of 32 elements, where each element is indexed by a name : eg : list_triplet_wells <-c("A1:A2:A3", "A4:A5:A6 ", "A7:A8:A9", "A10:A11:A12 ") xxx <-array(0, dim=4) dimnames(xxx) = list(list_triplet_wells) >From another

Re: [R] accessing the ellements in an array and factors.

1:A2:A3 A10:A11:A12 A4:A5:A6 A7:A8:A9 > xxx[yyy[1]] > A1:A2:A3 >0 > > Jim > > > On Fri, Jun 12, 2015 at 2:08 PM, David Winsemius > wrote: > > Cross-posting to SO and Rhelp is deprecated. > > > > On Jun 11, 2015, at 8:40 PM, Bogdan Tanasa wrote

[R] display a matrix in colors

Dear all, please could you advise about the most convenient functions or libraries to use in order to display a matrix as a heatmap/a color matrix ? the matrix contains the values of 0, 10, 20, 30 or 100. thank you ! -- bogdan [[alternative HTML version deleted]] __

Re: [R] display a matrix in colors

Hi David, thanks, yes, heatmap provides clustered heatmap, and I am looking for an unclustered display of a matrix, and only to set up the color ranges. thanks for your help ! -- bogdan On Fri, Jun 12, 2015 at 5:36 PM, David Winsemius wrote: > > > On Jun 12, 2015, at 5:28 PM, Bogd

Re: [R] display a matrix in colors

Fri, Jun 12, 2015 at 8:41 PM, Jim Lemon wrote: > Hi Bogdan, > Have a look at color2D.matplot in the plotrix package - it's a bit > different from "image" and "heatmap". > > Jim > > > On Sat, Jun 13, 2015 at 10:39 AM, Bogdan Tanasa wrote: &g

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

[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] 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

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 <

[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] 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, >

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

[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

[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

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] 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]]

[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

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])

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 >

[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

[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] 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." >

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

[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] 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

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

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

[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] 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] 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]] _

[R] a naive question

Hi, and my apologies for the following very naive question : I would like to read a column of numbers in R and plot a histogram. eg : x<-read.table("txSTART"); y<-as.numeric(x); and I do obtain the error : Error: (list) object cannot be coerced to type 'double'. Please could you let me know the

Re: [R] a naive question

Biostatisics > > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > On > Behalf Of Bogdan Tanasa > Sent: Wednesday, August 19, 2009 1:59 PM > To: r-help@r-project.org > Subject: [R] a naive question > > Hi, and m

[R] sequence clustering and assembly

Dear all, please could you suggest any R functions or packages (or external programs), that a. take as input a large number (> 10 000) of short 20-30 nt sequences, and do sequence assembly, to reconstruct larger (extended) 30-50 sequences ? b. take as input a larger number of sequences (100 000

[R] position weight matrix

Hi all, I am sorry to fill your inbox mail with a naive question, although I would really appreciate your opinion. I am looking for a R function that takes a set of aligned sequences, and transforms a position frequency matrix into a position weight matrix. Thanks a lot. -- bogdan [[alte

[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] 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

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, > >

[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] 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

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

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

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

>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

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

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

[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

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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 (

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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

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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] 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:

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