Re: [R] tcl tk: set the position button

Hi Rodrigo, Try to add tkgrid.configuration and change values as you want. library(tcltk2) win1 <- tktoplevel() butOK <- tk2button(win1, text = "TEST", width = 77) tkgrid(whiteSPACE, butOK, columnspan=2, padx=20, pady=10) tkgrid.configure(butOK,rowspan=2,columnspan= 3,sticky="nsew") Here is the d

[R] Spark DataFrame: replace NULL cell by NA

Dear All, ## function to relpace empty cell by NA empty_as_na <- function(x){ if("factor" %in% class(x)) x <- as.character(x) ## since ifelse wont work with factors ifelse(as.character(x)!="", x, NA) } ## connect to spark local sc <- spark_connect(master = "local") # load an example of datafra

[R] Convolutional neural networks (CNN) - build a model and After?

Hi, I am learning CNN using MXNet R package. I am following this great tutorial about olivetti_faces reconnaissance . In the end after building model and testing the final score was

Re: [R] Help with packages (methods, stats, stats4)

Yes, You are right. I mean install.packages('DVstats'). Actually, it seems that DVstats does not have maintainer https://github.com/USGS-R/DVstats Karim On Fri, Jan 12, 2018 at 7:20 PM, Duncan Murdoch wrote: > On 12/01/2018 1:11 PM, Karim Mezhoud wrote: > >> Hi, >>

Re: [R] Help with packages (methods, stats, stats4)

Hi, Did you try install.packages('stats'). Let we know about your Sys.info() Karim On Fri, Jan 12, 2018 at 5:37 PM, imane hajar wrote: > hello , > > i am so sorry , i figure it out. > > im sending this msj to the moderator to stop the approval of the mail . > > have a good day. > > > 2018-01-1

Re: [R] aggregate dataframe by multiple factors

Sorry, "That" and not "What". Best On Sun, Nov 20, 2016 at 9:00 PM, David Winsemius wrote: > > > On Nov 20, 2016, at 11:26 AM, Karim Mezhoud wrote: > > > > Many Thanks, > > What is exactly the solution. > > Is that a question? If s

Re: [R] aggregate dataframe by multiple factors

Many Thanks, What is exactly the solution. Best, Karim On Sun, Nov 20, 2016 at 8:17 PM, David Winsemius wrote: > > > On Nov 20, 2016, at 11:11 AM, David Winsemius > wrote: > > > > > >> On Nov 20, 2016, at 10:49 AM, Karim Mezhoud wrote: > >> >

Re: [R] aggregate dataframe by multiple factors

Yes the results does not have a date but successive DCE.1, DCE2, DCE.3 indicates DCE.date1 , DCE.date2, DCE.date3 I hope that the chronological order of date is conserved. Thanks, Karim On Sun, Nov 20, 2016 at 7:44 PM, David Winsemius wrote: > > > On Nov 20, 2016, at 5:28 AM, Kari

Re: [R] aggregate dataframe by multiple factors

0.540.59 0.57 > > however I wonder why the order according to the first row is necessary if > all NAs are on correct positions? > > Cheers > Petr > > > > -Original Message- > > From: R-help [mailto:r-help-boun...@r-project.org]

[R] aggregate dataframe by multiple factors

Dear all, the dat has missing values NA, first.Name Name Department DCE DP date 5 Auction VideosYME 0.57 0.56 2013-09-30 18 Amish WivesTAS 0.59 0.56 2013-09-30 34 Ancient NationQLH 0.54 0.58 2013-09-30 53 Auction VideosYME NA

Re: [R] Convert list to data frame

To known the format of your object, please use class(Data) str(Data) Be sure to have regular space between strings in your file.txt. Karim On Sat, Feb 27, 2016 at 3:56 PM, Ivan Calandra wrote: > Hi, > > I have seen this question a few days/weeks ago... > > Data.frames are special list, so it's

Re: [R] random number generation

Hi, This generate matrix: matrix( rnorm(5*4,mean=0,sd=1), 5, 4) for correlated matrix please see this link: http://stackoverflow.com/questions/10680658/how-can-i-create-a-correlation-matrix-in-r Karim On Wed, Nov 11, 2015 at 9:38 AM, leila zamani via R-help < r-help@r-project.org> wrote: > Hi e

Re: [R] Get the output of a function in R GUI

Hi, require(tcltk) data<-c(2,3,5,2) PressedOK <- function() { tkmessageBox(message=sum(data)) } tt <- tktoplevel() OK.but <- tkbutton(tt,text="OK",command=PressedOK) tkgrid(OK.but) tkfocus(tt) Please take a look in examples: http://mcu.edu.tw/~chenmh/teaching/project/r/reference/RTclTkExamples

Re: [R] Regex: Combining sub/grepl with ifelse

My code is not correct. The idea is to use apply instead of a loop. more efficiency. Karim On Sun, Oct 11, 2015 at 6:42 AM, Omar André Gonzáles Díaz < oma.gonza...@gmail.com> wrote: > Thanks Karim. linio.tv is in the email. In the last part. > El oct 11, 2015 12:39 AM, "Karim M

Re: [R] Regex: Combining sub/grepl with ifelse

Hi, omit unlist and test. otherwise you can use apply function. draft: df1 <- apply(linio.tv, 1, function(x) strsplit(x[,idproductio], "[^A-Z0-9-]+")) fct <- function(linio.tv){ if(any(grep("[A-Z][0-9]", linio.tv[,idx_productio]))) { linio.tv[,idx(id)] <- linio.tv[,idx

Re: [R] attribute color to a list

cter(attriColorValue(x,list,colors=c("blue","white","red"),feet=1))) > > There is probably a better name for your vector than "list". > > Jim > > > On Fri, Aug 28, 2015 at 8:16 PM, Karim Mezhoud wrote: > >> Hi, >> attriColorVa

[R] attribute color to a list

Hi, attriColorValue works with one value. I would like to get the color of a list with lappy but in input I have two variables (the value and the list). attriColorValue <- function(Value, list, colors=c(a,b,c, d,e),feet){ list <- round(list, digits = 0) Max <- max(list, na.rm=TRUE)

Re: [R] Global variables

normally that works, BUT <<- is BAD and not accepted in some repositories as Bioconductor. one<-function(){ a<-"variable passed" return(a) } x <- one() two<-function(x){ print(x) } On Tue, Jul 28, 2015 at 1:22 PM, jpara3 wrote: > Hi, I want to pass a variable value from one function to anoth

Re: [R] rename and color a list of list of list of values

s parent > list_parent <- function (i, n) { list(name=n, children=Map(list_child, i, > names(i)), colour=magic_colour(n)) } > > # get grandparent > grandparent <- Map(list_parent, expBefore, names(expBefore)) > > > Hope this helps! > > Best, S. > > >

[R] rename and color a list of list of list of values

Hi all, I have a list like this expBefore <- list(HM450=list(brac_tcga=list("ATM"=0.19,"ATR"=0.02,"BRCA1"=0.02,"BRCA2"=0.89,"CHEK1"=0.71,"CHEK2"=0.03), gbm_tcga=list("ATM"=0.19,"ATR"=0.02,"BRCA1"=0.02,"BRCA2"=0.89,"CHEK1"=0.71,"CHEK2"=0.03) ), HM27=list(brac_tcga=list("ATM"=0.19,

[R] new package: canceR

suggestions. Karim Mezhoud [[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-gu

Re: [R] tcltk problem

Hi, Here same working example. http://mcu.edu.tw/~chenmh/teaching/project/r/reference/RTclTkExamples/ Best, Karim On Wed, Mar 11, 2015 at 10:41 PM, Erich Neuwirth < erich.neuwi...@univie.ac.at> wrote: > OSX 10.10.2 > R 3.1.3 > XQuartz installed. > > I am trying to run one of the tcltk demos > Thi

Re: [R] R can't find tcl-tk

Hi,$I had this problem, delete all and reconfigure ONLY with: cd /tools ./rsyns. cd .. ./configure --enable-R-shlib make make install be sure to be in your /home kmezhoud On Wed, Mar 11, 2015 at 7:55 PM, peter dalgaard wrote: > > > On 11 Mar 2015, at 20:05 , MacQueen, Don wrote: > > > >

Re: [R] Rstudio R-devel libR.so

:sexp::Protect*) /home/ubuntu/rstudio/src/cpp/r/RExec.cpp: On Mon, Mar 9, 2015 at 10:53 AM, Pascal Oettli wrote: > Hello, > > There is a dedicated support to RStudio here: https://support.rstudio.com > > Regards, > Pascal > > On Mon, Mar 9, 2015 at 7:41 PM, Karim Mezhoud wrote

[R] Rstudio R-devel libR.so

bR.so (stable version R 3.1) to /usr/local/R-devel/lib/libR.so (R-devel version), That doesn't work. please find the detail at below. Karim mezhoud $which R /usr/bin/R $R > R.Version()[13] $version.string [1] "R version 3.1.2 (2014-10-31) > Sys.getenv("R_HOME") [1] &qu

Re: [R] install R-devel from R 3.1 to R 3.2 kubuntu

Resolved, Thanks sudo apt-get install libxt-dev sudo apt-get install fonts-inconsolata On Sun, Mar 8, 2015 at 11:30 AM, Uwe Ligges wrote: > > > On 08.03.2015 11:42, Karim Mezhoud wrote: > >> Thanks Uwe, >> yes I read it and I stopped on the last step (below). Somet

Re: [R] install R-devel from R 3.1 to R 3.2 kubuntu

; > On 08.03.2015 08:30, Karim Mezhoud wrote: > >> Dear all, >> I found some threads about compiling r-devel source and installing process >> but I need some clarifications. >> 1. Is it better to uninstall R 3.1 before installing R-devel? >> > > No,

[R] install R-devel from R 3.1 to R 3.2 kubuntu

Dear all, I found some threads about compiling r-devel source and installing process but I need some clarifications. 1. Is it better to uninstall R 3.1 before installing R-devel? 2. I have multiples library directories, R-devel will use these libpaths? > .libpaths() [1] "/home/mezhoud/R/x86_64-pc-l

Re: [R] remove repeated string in list

Many Thanks JS karim On Thu, Mar 5, 2015 at 4:08 AM, JS Huang wrote: > Hi, > > Here is one for preserving the first strings. as.numeric in the previous > posting is not necessary. > > > temp > $set1 > [1] "a" "b" "d" "x" > > $set2 > [1] "b" "c" "q" "m" > > $set3 > [1] "b" "f" "e" "k" "q" "h"

[R] remove repeated string in list

Dear All, here an example temp <- list(set1=c("a","b","d","x"), set2=c("b","c","q","m"), set3=c("b","f","e","k","q","h")) preserve only the first one string >temp set1 a b d x set2 c q m set3 f e k h OR remove repeated string >temp set1 a d x set2 c m set3 f e k h Thanks [[alternativ

Re: [R] Best Mac for R

Hi, It is not so efficient to have the most speed processor or biggest RAM. In general One processor is working at the time. It is more interesting to work with Linux for multiple multi_thread package and 64 bit. I am not sure if turbo boost is working with R. http://stackoverflow.com/questions/13

[R] Circlize package: add text to chord in symmetric matrix

Dear All temp matrix describes correlated genes by disease. Can I include which genes are common between diseases in chord diagram? > temp X1 X2Disease1Disease2Disease3 1 Gene1 Disease1 1. -0.31428571 0.25714286 2 Gene2 Disease1 1. 0.42857143 0.42857

Re: [R] compute values by condition in DF by rownames

Thanks JS I think aggregate function is better. Karim Le 17 févr. 2015 08:33, "JS Huang" a écrit : > Hi, > > I hope that someone can provide a better way to implement it. This is my > implementation. > > > data > X2 gbm_tcga lusc_tcga ucec_tcga_pub > 1 gbm_tcga 1.000

[R] compute values by condition in DF by rownames

Hi All, how to compute only abs(value) > 0.2 of DF X2 gbm_tcga lusc_tcga ucec_tcga_pub gbm_tcga 1.0 0.1405371906 -0.1028471639 gbm_tcga 1.0 0.0441343447 0.0135680550 gbm_tcga 1.0 -0.2000397119 0.0389718175 gbm_tcga 1.0 0.

[R] Extract data from Array to Table

Dear All, I am facing the task to extract data from array to table. here an example of array. ##Get A list of Matrices with unequal rows Disease <- NULL Diseases <- NULL ListMatByGene <- NULL for(i in 1:3){ Disease[[i]] <-matrix(sample(-30:30,25+(5* i)),5+i) rownames(Disease[[i]]) <- paste0("Sam

Re: [R] Rotate array by 90°

> [3,] "i" "f" "c" > > [[2]] > [,1] [,2] [,3] > [1,] "p" "m" "j" > [2,] "q" "n" "k" > [3,] "r" "o" "l" > > > > > Is this what you

Re: [R] Cube of Matrices or list of Matrices

Gene4 Disease3Disease2 0.5 Gene5 ... and Disease1 Disease2 Disease3 Disease1510 Disease21 53 Disease30 3 5 Thanks Karim On Tue, Jan 2

Re: [R] Rotate array by 90°

for(i in seq_len(nrow(x))) y[, i] <- rev(x[i, ]) > y > } > for(i in seq_len(n)) x <- r90(x) > x > } > > mat <- matrix(letters[1:9], byrow = TRUE, nrow = 3) > > rot90(mat) > rot90(mat, 3) > > > Hope this he

[R] Rotate array by 90°

Dear aal, Is there a way to rotate array or a cube of matrices by Y axis? MatLab example: A = cat(3,{'a' 'b' 'c';'d' 'e' 'f';'g' 'h' 'i'},{'j' 'k' 'l';'m' 'n' 'o';'p' 'q' 'r'}) A(:,:,1) = 'a''b''c' 'd''e''f' 'g''h''i' A(:,:,2) = 'j''k''l'

Re: [R] create a function with "subset" statement

Hi, You did the harder, it remains the easier listMatrices <- vector("list", 3) doAll <- function(A){ B <- subset(A, (A[,1] %in% c(1,2) & A[,2] %in% c(1,2)) | (A[,1] %in% c(3)& A[,2] %in% c(1) ) | (A[,1] %in% c(4)& A[,2] %in% c(1:4)) ) C <- s

Re: [R] Cube of Matrices or list of Matrices

8:22 PM, Ben Tupper wrote: > Hi again, > > On Jan 19, 2015, at 1:53 PM, Karim Mezhoud wrote: > > Yes Many thanks. > That is my request using lapply. > > do.call(cbind,col1) > > converts col1 to matrix but does not fill empty value with NA. > > Even for &

Re: [R] Cube of Matrices or list of Matrices

/ /'_;kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ On Mon, Jan 19, 2015 at 4:36 PM, Ben Tupper wrote: > Hi, > > On Jan 18, 2015, at 4:36 PM, Karim Mezhoud wrote: > > > Dear All, > > I am trying to get correlation between Diseases (80) in columns and > > s

[R] Cube of Matrices or list of Matrices

Dear All, I am trying to get correlation between Diseases (80) in columns and samples in rows (UNEQUAL) using gene expression (at less 1000,numeric). For this I can use CORREP package with cor.unbalanced function. But before to get this final matrix I need to load and to store the expression of 1

Re: [R] Rstudio and GIT

Hi, I think you need to open your project after In RStudio, go to project options, then to the Git/SVN panel. Change the “Version control system” from “None” to “Git”: http://r-pkgs.had.co.nz/git.html#git-status Karim Ô__ c/ /'_;kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/

Re: [R] Help on Principal Component Analysis in R

Hi error message indicates that you have non numeric value in your table/ matrix. Replace missing value by NA and add na.rm= true in your command prcomp. Karim Le 14 janv. 2015 00:27, "R Help!" a écrit : > Hello! > > I am a beginner to R. I have read several guides, but still am stuck on > this:

Re: [R] Overlapping Matrices By column correlation

#. with > /Software/Embedded Controllers) .OO#. .OO#. rocks...1k > --- > Sent from my phone. Please excuse my brevity. > > On January 9, 2015 7:57:02 AM PST, Karim Mezhoud > wrote

Re: [R] Overlapping Matrices By column correlation

Thanks David. It seems not easy to compare multiple Matrices. karim Ô__ c/ /'_;kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ On Thu, Jan 8, 2015 at 6:40 PM, David Winsemius wrote: > > On Jan 8, 2015, at 2:26 AM, Karim Mezhoud wrote: > > > Mantel tes

[R] Overlapping Matrices By column correlation

Mantel test is interesting but it can't displays wish columns are similar. Here an example: M gene1 gene2 gene3 gene4 gene5 Sample1 241 72 Sample2 0 NA2.3 19 Sampl

Re: [R] Fwd: which is faster "for" or "apply"

0.81 0.786 0.596 0.861 0.646 ... >$ HPGDS: num 0.576 0.528 0.703 0.781 0.622 ... >$ MDC1 : num 0.189 0.265 0.201 0.199 0.249 ... >$ MLH1 : num 0.404 0.0192 0.017 0.0124 0.0197 ... >$ MS4A2: num 0.913 0.898 0.937 0.861 0.768 ... >$ MSH2 : num 0.018 0.0184 0

Re: [R] Fwd: which is faster "for" or "apply"

for both cidx <- !(sapply(df, is.numeric)) df[cidx] <- lapply(df[cidx], as.numeric) Ô__ c/ /'_;kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ On Wed, Dec 31, 2014 at 5:51 PM, Karim Mezhoud wrote: > Yes the last one this the best. But I need to test if retur

Re: [R] Fwd: which is faster "for" or "apply"

ileData(cgds,GeneList, > "stad_tcga_methylation_hm450","stad_tcga_methylation_hm450")) > > > With my computer I did not find the same structure (numeric vs factor). > > Also I need to preserve row and column names ;) > So I am working to resolve these details

Re: [R] Fwd: which is faster "for" or "apply"

find the same structure (numeric vs factor). Also I need to preserve row and column names ;) So I am working to resolve these details depending on data of cbioportal... Thank you Ô__ c/ /'_;kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ On Wed, Dec 31, 2014 at 4:37

Re: [R] Fwd: which is faster "for" or "apply"

> On 12/31/2014 12:22 AM, Karim Mezhoud wrote: > >> Thanks, >> It seems for loop spends less time ;) >> >> with >> dim(DataFrame) >> [1] 338 70 >> >> For loop has >> user system elapsed >>0.012 0.000 0.012 >> >&

[R] Fwd: which is faster "for" or "apply"

, Dec 31, 2014 at 8:54 AM, Berend Hasselman wrote: > > > On 31-12-2014, at 08:40, Karim Mezhoud wrote: > > > > Hi All, > > I would like to choice between these two data frame convert. which is > > faster? > > > > for(i in 1:ncol(DataFrame)){ >

[R] which is faster "for" or "apply"

Hi All, I would like to choice between these two data frame convert. which is faster? for(i in 1:ncol(DataFrame)){ DataFrame[,i] <- as.numeric(DataFrame[,i]) } OR DataFrame <- as.data.frame(apply(DataFrame,2 ,function(x) as.numeric(x))) Thanks Karim Ô

Re: [R] NA problem in rbind of an apply summary

Hi, Could you try rbind.na.R function. karim Ô__ c/ /'_;kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ On Wed, Dec 10, 2014 at 10:34 PM, Raffaello Vardavas wrote: > Dear All, > > I have a data fame. Each column has numerical values but some columns may > have NA values. >

Re: [R] function to avoid <<-

this query and the responses. You all just helped me to > eliminate the use of global variables from my R package. I knew they were > not recommended, but I didn't know how to get around using them. > > Thanks! > > Jean > > On Tue, Dec 2, 2014 at 10:59 AM, Karim M

Re: [R] function to avoid <<-

the R session). Further, when this code > is compiled into a package then "myenv" becomes package local, meaning that > functions within the package can access it and the objects inside of it, > but it will not interfere with any other packages or the global environment. >

Re: [R] function to avoid <<-

a() in that way. Perhaps you want > R/sysdata.rda. See http://r-pkgs.had.co.nz/data.html for more details. > > Hadley > > On Tue, Dec 2, 2014 at 2:28 AM, Karim Mezhoud wrote: > > Dear All, > > > > I am writing a GUIpackage that needs global variables. > > I ha

[R] function to avoid <<-

Dear All, I am writing a GUIpackage that needs global variables. I had many warning message when I checked the code as for example: geteSet: no visible binding for global variable ‘curselectCases’ I would like to write a function that creates a global place for Objects to be loaded as: Fun <- fu

Re: [R] rpart package: How can I save print(rpart)

unlap > TIBCO Software > wdunlap tibco.com > > On Thu, Nov 13, 2014 at 1:13 PM, Karim Mezhoud wrote: > >> Yes Thanks! that works, >> but I loose the \n when I would like to save or edit it. >> >> getTextInWindows is a function that edits any text in editor. >&g

Re: [R] rpart package: How can I save print(rpart)

t; [1] " Min. 1st Qu. MedianMean 3rd Qu.Max. " > [2] " 1.003.255.505.507.75 10.00 " > > cat(junk, sep="\n") > Min. 1st Qu. MedianMean 3rd Qu.Max. > 1.003.255.505.50 7.75 10.00 > &

[R] rpart package: prp does not work with RStudio and R console

Hi, All right for rpart package but it seems there is a confusion in "text" function. prp is not found Error in fun() : could not find function "prp" Thanks Ô__ c/ /'_;kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ [[alternative HTML version deleted]] ___

[R] rpart package: How can I save print(rpart)

Hi, the print of rpart fitting gives the summary of tree I would like to save the console text of: fit <- rpart(formula, data) summary <- print(fit) when I look in "summary" I did not find the same thing as in "print(rpart)" [1] "Clinical Data exists" [1] "merging samples from Clinical an

Re: [R] EM algorithm for ARIMA models

EBarrays http://www.bioconductor.org/packages/release/bioc/html/EBarrays.html Ô__ c/ /'_;kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ On Fri, Nov 7, 2014 at 4:23 PM, Mathias Martens wrote: > Hi there,I am working on a time series dataset with a lot of missing data > (aro

[R] matching genes to a list of gene groups an built binary data frame

Dear All, I have a gene list Genes <- c("ACACA", "BAX" , "BCL2", "BID", "BAX", "MAPK9") and a list of group of genes ListGroup <- list(group1=c("ACACA" ,"AHSA1" ,"AIMP2", "AKR1B1", "AKT1", "AKT1S1"), group2=c("ANXA1" , "AR" , "ARID1A" , "ATM" , "BAK1" , "BAX" ), g

[R] Desktop icon to run R and load/run specific package

Hi, I'm developing R package with GUI. I would write a file that run R and load package by double clic. I am using Kubuntu. If there is a solution with windows or mac, I am interested too. Thanks Karim [[alternative HTML version deleted]] __ R-h

[R] Built R package with example

Dear All, How can I add folder content examples of needed files to run example? The simple add of folder did not built and reload with the package. Thanks! Karim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https:/

[R] buit a package using Rstudio and existing R files

Dear All, I am trying to built for the first time a package. I am following this tutorial: https://support.rstudio.com/hc/en-us/articles/200486488-Developing-Packages-with-RStudio I create a new Project (package) and I added 44 .R sources files (functions). After, I got error message when I built