[R] Need help on creating Adjacency matrix in R

Hello everyone I am relatively new to R and wanted some help on creating adjacency matrix I have a dataset as given below and wanted to create an adjacency matrix in R. For creating an adjacency matrix, the matrix should be a square matrix. I tried creating a matrix directly, but it would not be

Re: [R] Problems with R package building

On Jun 14, 2013, at 7:18, jpm miao wrote: > Hi, > > I try to build a toy package by running the following codes in an R > program > > require(stats) > f <- function(x,y) x+y > g <- function(x,y) x-y > d <- data.frame(a=1, b=2) > e <- rnorm(1000) > package.skeleton(list=c("f","g","d","e"), na

[R] how to output the data array without colname and row number

hi r users: I have a datadset and want to write into a file . when i use : write.table(u_bar, file = "u_test.txt") the data in the outpuf file is shown as below which included the row number from "1" to "14" and colname .e.g."X32N" How could I output the numbers and excluded the colname and ro

Re: [R] how to output the data array without colname and row number

how about reading the help file on 'write.table' and look at row.names and col.names. Sent from my iPad On Jun 14, 2013, at 3:27, Jie Tang wrote: > hi r users: > I have a datadset and want to write into a file . > > when i use : > write.table(u_bar, file = "u_test.txt") > > the data in the

Re: [R] How to get a running mean result by R?

Hello, As for Inf, the mean value of Inf and anything is Inf, so there's no way to solve it. As for NaN, you can set them to NA prior to calling the function. That leaves us with NA handling. forecast::ma handles NAs, it propagates them, as it should. An alternative function using filter() lik

[R] Problem in Matrix

Hello, Suppose, I have P = 100 genes variables and each consists of n = 50 values. Now I want to Bootstrap (With Replacement) 50 times and 100 iterations. I want P in columns and Bootstrap iterations in Rows. Also, when genes are selected in Bootstrap (WR) give it value "1", if not selected "0".

[R] Problem in linking a library in R package

Hello everyone , I am facing a simple problem , I trying to add functionality in one of R package . I want a profiling library to link to R package so that when R package is used the profiling out put comes automatically with that. Problem is that I am not able to link it with the package , I trie

[R] rename and concatenate name of columns

Dear all, I have different data frames for which I would like to modify names of each column such that the new name would include the name of the first column added to the name of other columns; I came up with the following code. Nothing changes when I run the following code. I would be grateful i

Re: [R] Need help on creating Adjacency matrix in R

HI, May be this helps: dat1<- read.table(text=" Col1 Col2 Weight   A D 0.1   B C 0.4   C M 0.6   D P 0.8   E W 1   F D 1.2   G C 3.1   H M 4 ",sep="",header=TRUE,stringsAsFactors=FALSE)  vec1<- c(unique(dat1[,1]),unique(dat1[,2])) datNew<- expand.grid(vec1,vec1) colnames(datNew)<- colnames(dat1)

Re: [R] Problem in linking a library in R package

On 13-06-14 3:47 AM, Gaurav Sehrawat wrote: Hello everyone , I am facing a simple problem , I trying to add functionality in one of R package . I want a profiling library to link to R package so that when R package is used the profiling out put comes automatically with that. Problem is that I am

Re: [R] rename and concatenate name of columns

Hi, rename_columns<- function(dat){     for(i in 2:(ncol(dat))){     names(dat)[i]<- paste(names(dat)[1],names(dat)[i],sep="_")         } dat } dat1<- read.table(text=" chr    pos    ref    alt chr1    5    A    G chr1    8    T    C chr2    2    C    T ",sep="",header=TRUE,stringsAsFactors=FALSE

Re: [R] rename and concatenate name of columns

On Fri, Jun 14, 2013 at 10:01 AM, arun wrote: > Hi, > rename_columns<- function(dat){ > for(i in 2:(ncol(dat))){ > names(dat)[i]<- paste(names(dat)[1],names(dat)[i],sep="_") > > } > dat > } Or even better, get rid of the unnecessary loop: rename_columns <- function(DF) { names(DF

[R] Removing "NA" from matrix

Dear R forum, I have a data frame dat = data.frame( ABC = c(25.28000732,48.33857234,19.8013245,10.68361461), DEF = c(14.02722251,10.57985168,11.81890316,21.40171514), GHI = c(1,1,1,1), JKL = c(45.96423231,44.52986236,16.56514176,32.14545122), MNO = c(45.38438063,15.54338206,18.78444777,24.29486

Re: [R] rename and concatenate name of columns

Thanks all! On Fri, Jun 14, 2013 at 6:40 PM, Rainer Schuermann < rainer.schuerm...@gmx.net> wrote: > df1 <- data.frame( A = runif( 10 ), B = runif( 10 ) * 5, C = runif( 10 ) * > 10, D = runif( 10 ) * 20 ) > df2 <- data.frame( X = runif( 10 ), Y = runif( 10 ) * 5, Z = runif( 10 ) * > 10 ) > renam

Re: [R] Removing "NA" from matrix

HI, Try: dat1<-dat[sapply(dat,function(x) length(unique(x)))>1] cor(dat1) #   ABC DEF JKL    MNO #ABC  1.000 -0.75600764  0.55245223 -0.2735585 #DEF -0.7560076  1. -0.06479082  0.2020781 #JKL  0.5524522 -0.06479082  1.  0.4564568 #MNO -0.2735585  0.2

Re: [R] Removing "NA" from matrix

Probably, this also works: dat2<-dat[,(colSums(dat)/dat[1,])!=nrow(dat)] cor(dat2) dat$NewCol<-5  dat3<-dat[,(colSums(dat)/dat[1,])!=nrow(dat)]  cor(dat3) #   ABC DEF JKL    MNO #ABC  1.000 -0.75600764  0.55245223 -0.2735585 #DEF -0.7560076  1. -0.06479082 

Re: [R] rename and concatenate name of columns

df1 <- data.frame( A = runif( 10 ), B = runif( 10 ) * 5, C = runif( 10 ) * 10, D = runif( 10 ) * 20 ) df2 <- data.frame( X = runif( 10 ), Y = runif( 10 ) * 5, Z = runif( 10 ) * 10 ) rename_columns <- function( dataset ) { for( i in 2:ncol( dataset ) ) colnames( dataset )[i]

Re: [R] find the position of first observation for each subject

I would typically use rle() for this kind of thing: > tmp <- cumsum(rle(id)$lengths) > c(1, tmp[-length(tmp)]+1) [1] 1 4 9 It does assume that all rows for each unique value of id are grouped together, but does not require that the rows be sorted by id. -Don -- Don MacQueen Lawrence Livermor

Re: [R] Removing "NA" from matrix

On Jun 14, 2013, at 7:03 AM, Katherine Gobin wrote: > Dear R forum, > > I have a data frame > > > dat = data.frame( > ABC = c(25.28000732,48.33857234,19.8013245,10.68361461), > DEF = c(14.02722251,10.57985168,11.81890316,21.40171514), > GHI = c(1,1,1,1), > JKL = c(45.96423231,44.52986236,16.5

Re: [R] rename and concatenate name of columns

On Jun 14, 2013, at 6:34 AM, Arman Eshaghi wrote: > Dear all, > > I have different data frames for which I would like to modify names of each > column such that the new name would include the name of the first column > added to the name of other columns; I came up with the following code. > Noth

Re: [R] Problem in linking a library in R package

I have posted the question on stackoverflow but no satisfied there. Here is the Link : http://stackoverflow.com/questions/17049966/how-to-include-a-shared-library-so-or-library-in-a-r-package Thanks On Fri, Jun 14, 2013 at 7:15 PM, Duncan Murdoch wrote: > On 13-06-14 3:47 AM, Gaurav Sehrawat wr

[R] How to interactively create manually guided Decision Tree

I am new in using R. I want to know all about building decision tree model in R. Few options which I searched are rpart and rattle to build a decision tree.Both the functions are giving me splits which are statistically appropriate. But I am not able to figure out how to change those splits as p

[R] R session freezes when I try to save a new script

All: Recently my R session freezes when I try to open a file or save a new script after I have run existing scripts. The session freezes so that I can no longer click on any windows within the R session -- including other scripts that are open or the R console. (I hear the "ding" sound when

Re: [R] R session freezes when I try to save a new script

It would probably help if you posted your sessionInfo() Just before everything freezes issue the command sessionInfor() copy the output and paste it into an email. John Kane Kingston ON Canada > -Original Message- > From: anferg...@aol.com > Sent: Fri, 14 Jun 2013 10:52:03 -0400 (EDT

[R] Trying to get the 'Digitize' package

Dear R users, I'm trying to get the 'Digitize' package but it has been removed from the CRAN repository. I tried to download the .tar.gz file from the archive but I haven't been able to install it. Anyone has a clue on how I could proceed to access this package? Thanks Jean-Michel Fortin Univers

Re: [R] How to interactively create manually guided Decision Tree

You need to do some reading, both about decision trees and R! What you need to do for R is to use cut() on Age (?cut) to create a new categorical variable, ageCat, say, and then use that in your tree building instead of Age. Cheers, Bert On Fri, Jun 14, 2013 at 7:24 AM, Neelesh Gupta wrote: > I

Re: [R] Trying to get the 'Digitize' package

You can check the archive section of your CRAN mirror to see if there are older versions of the package there that may work for you. An alternative approach if you have a graphics file of a plot that you want to extract the data from by clicking on the points (ignore the rest of this if I am misre

[R] MS Access

Dear guRus Can I use R inside Microsoft access Macros and programmes? I understand that R-Excel is compatible but wish to know if I can use R inside Access programmes please? Many thanks Raghu [[alternative HTML version deleted]] __ R-help@r-p

Re: [R] MS Access

On Jun 14, 2013, at 10:04 AM, Raghuraman Ramachandran wrote: > Dear guRus > > Can I use R inside Microsoft access Macros and programmes? I understand > that R-Excel is compatible but wish to know if I can use R inside Access > programmes please? > RExcel has a separate mailing list. You should

Re: [R] R session freezes when I try to save a new script

You will probably need to read the Posting Guide and follow its recommendations to get a constructive response. Things like posting in text instead of HTML and providing the output of sessionInfo go a long way toward speeding up the troubleshooting process. You can also begin the process of ide

Re: [R] survreg with measurement uncertainties

Hrm, thanks. The uncertainties are what they are, though (and the model is what it is, too) -- is there an alternative to modifying them? Maybe another type of analysis that handles upper limits? Kyle On Thu, Jun 13, 2013 at 5:46 AM, Andrews, Chris wrote: > It seems a line through the origin d

[R] addtable2plot problem with adding summary object

Hello, I am trying to add a summary generated by summary () to a plot.The output of the summary is an object of class (summaryDefault,table) When I try to add it with addtable2plot (x="topright",sum_1) I get an error:Error in dim(table) : 'table' is missing Here is some info about sum_1:> print

Re: [R] rename and concatenate name of columns

For the record: ... > > A bit of commentary: Something did happen. It's just that you didn't do > anything with _what_ happened. The copy of the 'dataset'-object got modified > but you never returned it from the function, and and also didn't reassign it > to the original 'dataset'

Re: [R] matched samples, dataframe, panel data

Hi, I changed the fun1().  Now, it should be possible to get all the possible combinations within each group. final3New<-read.table(file="real_data_cecilia.txt",sep="\t",header=T) final3New1<-read.csv("real_data_cecilia_new.csv") fun1New<- function(dat,percent,number){     lst1<- split(dat,list(

[R] combination of columns in a matrix

Hello, I have a matrix m and I want to know how often does 1 (or !0) simultanously appear in A and REF, B and REF, C and REF. So actually I wish to automate following expression: > length (which (m[,1]!=0&m[,4]!=0)) [1] 2 > length (which (m[,2]!=0&m[,4]!=0)) [1] 1 Thanks Hermann > m A B C

[R] significance testing for the difference in the ratio of means

I have a question regarding significance testing for the difference in the ratio of means. The data consists of a control and a test group, each with and without treatment. I am interested in testing if the treatment has a significantly different effect (say, in terms of fold-activation) on the te

Re: [R] combination of columns in a matrix

Hi, sapply(colnames(m)[-ncol(m)],function(i) {x1<-cbind(m[,i],m[,ncol(m)]); length(which(x1[,1]!=0 & x1[,2]!=0))}) #A B C #2 1 2 A.K. - Original Message - From: Hermann Norpois To: r-help Cc: Sent: Friday, June 14, 2013 3:51 PM Subject: [R] combination of columns in a matrix Hello

Re: [R] significance testing for the difference in the ratio of means

Sigh... (Again!) These are primarily statistical, not R, issues. I would urge that you seek local statistical help. You appear to be approaching this with a good deal of semi-informed adhoc-ery. Standard methodology should be applicable, but it would be presumptuous and ill-advised of me to offer

Re: [R] rename and concatenate name of columns

On Jun 14, 2013, at 1:25 PM, Bert Gunter wrote: > For the record: > > ... > > >> >> A bit of commentary: Something did happen. It's just that you didn't do >> anything with _what_ happened. The copy of the 'dataset'-object got modified >> but you never returned it from the funct

[R] "Error: cannot allocate vector of size 1.9 Gb" when loading xtable help

I am using xtable version 1.7-1 built for R 3.0.1 on: R version 3.0.1 (2013-05-16) Platform: i686-pc-linux-gnu (32-bit) Sometimes, not every time, when I load xtable or attempt to load the help, I get an error such as this "Error: cannot allocate vector of size 1.9 Gb" (Stacktrace from recover()

Re: [R] significance testing for the difference in the ratio of means

My apologies if my request is off topic and for my admittedly half-baked understanding of the topic. I'm afraid trying to talk with the "local statistical help", and trying to post on several general statistical forums to look for proper guidance has not yielded any response much less any helpful

Re: [R] significance testing for the difference in the ratio of means

The fact that your currents are apparently intrinsically positive and the variance increases with current plus the fact that you are interested in ratio statistics suggests that your data would benefit from an initial log transform of the data. All of your issues would then disappear, given tha

[R] checking certain digits of a number in a column

Hi, I need to check whether certain digits of a number, say, last five digits, appear in a column of a data frame. For instance, For example,103 in "000103" ( data [data[,3] == "...103"] instead of data [data[,3] == "000103"] ) or 54780 in "12354780". Can someone let me know how to do so. Thank

Re: [R] checking certain digits of a number in a column

On Jun 14, 2013, at 9:33 PM, Yasin Gocgun wrote: > Hi, > > I need to check whether certain digits of a number, say, last five digits, > appear in a column of a data frame. For instance, > > For example,103 in "000103" ( data [data[,3] == "...103"] instead of > data [data[,3] == "000103"] ) or

Re: [R] checking certain digits of a number in a column

Try ?grep or library( stringr ) ?str_detect On Saturday 15 June 2013 00:33:31 Yasin Gocgun wrote: > Hi, > > I need to check whether certain digits of a number, say, last five digits, > appear in a column of a data frame. For instance, > > For example,103 in "000103" ( data [data[,3] == "...