[R] gsub and multiple replacements

Hi, I would like to replace "A B" by "A-B" and "AA(DD)" by "AA" using a single gsub. Is that possible besides using two gsub ? Thanks Stanley [[alternative HTML version deleted]] __ R-help@r-project.org mailing list htt

[R] How to get subset of rows and columns that are most strongly correlated ?

Hi, I have a relatively large matrix 20k rows and 1000 columns. Instead of trying all possible combinations, is there a way to identify subset of rows and columns that are most strongly correlated ? Thanks Stanley [[alternative HTML version deleted]]

[R] Optimization problem, to minimize the length(rle(B)$lengths) for all the rows and columns

Hi, how can I order the rows and columns of a matrix A to generate B, in order to minimize the length(rle(B)$lengths) for all the rows and columns ? > set.seed(5) > a <- matrix(rnorm(200), nrow=20) > a[a<=0] <- 0 > a[a>0] <- 1 > a [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,]

[R] 3 questions: debug R script, multi-level sorts, and multi-gsub

Hi, 1) I ran a script say test.R. It ran and terminated with an error. However, I am not sure where the error occur. > source("test.R") Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see

[R] How to insert a vector or matrix into an existing matrix

Hi, Is there any functions to insert a vector or matrix into an existing matrix say between row 5 and 6 or column 8 and 9, without creating a temporary matrix ? Thanks Stanley [[alternative HTML version deleted]] __ R-help@r-project.org mailin

[R] Is there any function to skip a loop in a for loop ?

Hi, Is there any function to skip a loop in a for loop ? Thanks Stanley [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-projec

Re: [R] What objects will save.image saves ? And how to specify objects to be saved..

Read and reread, can't make out. Will try an experiment later On Wed, Apr 16, 2008 at 7:51 PM, Henrique Dallazuanna <[EMAIL PROTECTED]> wrote: > See ?save > > On Wed, Apr 16, 2008 at 8:46 AM, Ng Stanley <[EMAIL PROTECTED]> > wrote: > > > Hi, > &g

[R] What objects will save.image saves ? And how to specify objects to be saved..

Hi, I have a R script that loads an image R.data, does some operations, then save to the R.data again. Suppose I have done some computation before loading the R script, will all the objects before the R script execution be saved to R.data ? If yes, how can I specify save.image to save only those o

Re: [R] How to get assign an vector of words to associative array ?

Thanks that help. On Wed, Apr 16, 2008 at 8:46 AM, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > On 15/04/2008 8:36 PM, Ng Stanley wrote: > > > Hi, > > > > How to get assign an vector of words to associative array ? > > > > a[["animal"]] <

[R] How to test if t[["cat"]] exists ?

Hi, > t <- list("cat"=1) > exists("t") [1] TRUE > exists("t[["cat"]]") Error: unexpected symbol in "exists("t[["cat" > exists("t[[\"cat\"]]") [1] FALSE Thanks Stanley [[alternative HTML version deleted]] __ R-help@r-project.org mailing list ht

[R] How to get assign an vector of words to associative array ?

Hi, How to get assign an vector of words to associative array ? > a[["animal"]] <- c("dog", "cat") Error in a[["animal"]] <- c("dog", "cat") : more elements supplied than there are to replace Thanks stanley [[alternative HTML version deleted]]

[R] reusing custom functions, how to ?

Hi, I have created a number of custom functions, and hope to reuse them in other source files. How should I go about doing that ? Thanks Stanley [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mai

[R] p-values always identical for t.test of certain group of samples, why ?

Hi, Given the following, a <- rnorm(5) b <- rnorm(5) c <- rnorm(5) a.1g.scale <- scale(c(a,b,c))[1:5] b.1g.scale <- scale(c(a,b,c))[6:10] c.1g.scale <- scale(c(a,b,c))[11:15] a.2g.scale <- scale(c(a,b))[1:5] b.2g.scale <- scale(c(a,b))[6:10] c.2g.scale <- scale(c) a.3g.scale <- scale(a) b.3g.scal

[R] how to write a table to pdf

Hi, Is there a way to write a table to pdf ? I have checked write.table, it only writes to text file. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the post

Re: [R] Initialize many variables to NUL, check whether an object exist

Hi, How can I force the assignment ? > RG[["ABC"]] <- c("a", "b") Error in RG[["ABC"]] <- c("a", "b") : more elements supplied than there are to replace On Mon, Apr 14, 2008 at 9:53 PM, Gabor Csardi <[EMAIL PROTECTE

[R] Initialize many variables to NUL, check whether an object exist

Hi, Two questions: A) I need to initialize many variables to NULL. So I created variable_names <- c("a1", "a2"). What can I do to variable_names so that variable a1 is NULL and a2 is NULL ? B) How can I check whether an object exist ? Thanks Stanley [[alternative HTML version deleted]]

Re: [R] Associative array and How to store a set of objects ?

2008 at 08:32:55PM +0800, Ng Stanley wrote: > > Hi, > > > > Two questions: > > > > A) Assuming OB is an object, how do I store 20 of OB in a vector or list > ? > > replicate(20, OB, simplify=FALSE) > > > B) Does R has something similar associative

[R] Associative array and How to store a set of objects ?

Hi, Two questions: A) Assuming OB is an object, how do I store 20 of OB in a vector or list ? B) Does R has something similar associative array to Perl ? For example, %our_friends = ('best', 'Don', 'good', 'Robert', 'worst', 'Joe'); $our_friends{'cool'} = "Karen"; Thanks Stanley [[alter

Re: [R] How to refer to rows using a vector of row names ?

That should work well too if my row names are integers only. However, they are strings of alphanumeric characters On Fri, Apr 11, 2008 at 7:56 PM, Philipp Pagel <[EMAIL PROTECTED]> wrote: > On Fri, Apr 11, 2008 at 07:00:10PM +0800, Ng Stanley wrote: > > I tried that, it will w

Re: [R] How to refer to rows using a vector of row names ?

I tried that, it will work well if the vector contain unique row names. However, my vector contain duplicate row names. On Fri, Apr 11, 2008 at 6:53 PM, Petr PIKAL <[EMAIL PROTECTED]> wrote: > Hi > > > [EMAIL PROTECTED] napsal dne 11.04.2008 12:46:11: > > > Hi, > > > > How to refer to rows using

[R] How to refer to rows using a vector of row names ?

Hi, How to refer to rows using a vector of row names ? Thanks Stanley [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.

[R] Beautifying axis tick labels

Hi, For example, the y axis shows "0 50 150". Is there any way to beautify the tick labels to get 0 5 10 15, and at the top of y-axis "x10^5" (superscript 5) ? My plots all have different ylim, how to perform the beautification automatically ? Thanks Stanley [[alternative HTML ve

[R] legend placement

Hi, I am plotting 5 charts using p <- par(mfrow = c(3, 2), how can I place my legend in the last region ? I don't wan to put it into the margin. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mail

Re: [R] I have a 3 by 2 plots per page. How do I specify a title at the top centre of each page ?

Found the solution, p <- par(mfrow = c(3, 2), oma = c(0, 0, 2.1, 0)) title(main = paste("Title is here"), outer = TRUE, cex.main = 1.5, font.main = 4) On Thu, Apr 10, 2008 at 11:20 AM, Ng Stanley <[EMAIL PROTECTED]> wrote: > Hi, > > I have a 3 by 2 plots per page.

[R] I have a 3 by 2 plots per page. How do I specify a title at the top centre of each page ?

Hi, I have a 3 by 2 plots per page. How do I specify a title at the top centre of each page ? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guid

[R] How to create a legend without plot, and to use scientific notation for axes label ?

Hi, I have a 3 by 2 plots per page, and would like to place a legend on the last region. How to do that ? Also, is there any way to specify scientific notation for axes label ? [[alternative HTML version deleted]] __ R-help@r-project.org maili

[R] Correlation between two multi-dimensional matrices

Hi, Are there any methods for computing the correlation between two multi-dimensional matrices ? Will transforming the matrices into vectors and applying pearson be fine ? Any blind spots that I should be aware ? Thanks Stanley [[alternative HTML version deleted]] __

[R] conditional matching of rows of tables

Hi, Given matrix A of 4 cols. 1 a 0 4 1 b 5 8 2 a 0 3 2 b 4 7 I have another matrix B of 3 cols. How to assign (a or b) to the rows such that in each row its 1st value must match the 1st col. of A, 2nd and 3rd values must lie between 3rd and 4rd cols (inclusive) of A 1 2 3 -> a 2 4 5 -> b 2 0 3

[R] How to plot the dendrogram or tree for kmeans ?

Hi, How to plot the dendrogram or tree for kmeans, like we do for hclust ? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-proj

[R] How to get the value of last element in a vector/array ?

Hi, a[length(a)] gives the value of last element. Is there an alternative without using functions ? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the postin

[R] Where are the latest html help for R, base packages and Bioc packages ?

Hi, Can anyone direct me ? Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide c

Re: [R] How to turn a string into a variable name ?

s[[2]]) > > [1] 2 4 6 8 10 > > > > > > Bill Venables > > CSIRO Laboratories > > PO Box 120, Cleveland, 4163 > > AUSTRALIA > > Office Phone (email preferred): +61 7 3826 7251 > > Fax (if absolutely necessary): +61 7 3826 7304 > > Mobil

[R] How to turn a string into a variable name ?

Hi, For example, natural_nums <- 1:10 even_nums <- seq(2,10, by = 2) types <- c("natural_nums", "even_nums") What functions can be performed on types[1] to turn it into a variable name and not a string ? [[alternative HTML version deleted]] _

[R] how to generate bar charts with the standard deviation

Hi, I have the two vectors mean and sd of individual columns, but I am unsure how to generate bar charts with the standard deviation, even after looking the help of barplot and barplot.2. [[alternative HTML version deleted]] __ R-help@r-project

[R] How to manipulate data according to groups ?

Hi, I have a two columns data, the first column are values, and second column are the groups. For this example, there are 3 groups 1,2,3. How can I manipulate the values in the first column according to groups, say I would like to find mean, sum, and standard deviation for the different groups ?

[R] How to cbind or rbind different lengths vectors/arrays without repeating the elements of the shorter vectors/arrays ?

Hi, How to cbind or rbind different lengths vectors/arrays without repeating the elements of the shorter vectors/arrays ? > cbind(1:2, 1:10) [,1] [,2] [1,]11 [2,]22 [3,]13 [4,]24 [5,]15 [6,]26 [7,]17 [8,]28 [9,]1

[R] How to specify where add-on packages should be installed

Hi, I am running R on a cluster. Basic packages are installed at ~/MyHome/lib64/R/library/ and add-ons packages are installed at ~/R/x86_64-redhat-linux-gnu-library/2.5/. Both directories were created by R by default. Problems arises when I use add-on packages, R complains that they can't be foun

[R] How to generate a vector of counts i.e. the number of rows that are contiguous

Hi, I have a 3 columns data and need to generate a vector of counts. These counts are the number of rows that are contiguous. It looks easy for manual counting, but to turn it algorithmic really split my head. For example, 11 (i.e. 18004 to 180014), 1 (i.e., 18017), 7 (i.e., 18060 to 18064) 1800

Re: [R] How to generate column names for pairwise comparison

> Best, > Dimitris > > > Dimitris Rizopoulos > Biostatistical Centre > School of Public Health > Catholic University of Leuven > > Address: Kapucijnenvoer 35, Leuven, Belgium > Tel: +32/(0)16/336899 > Fax: +32/(0)16/337015 > Web: http://med.kuleuven.be

[R] How to generate column names for pairwise comparison

Hi, Given names <- c("a", "b", "c", "d"). I would like to generate "a vs. b", "a vs. c", "a vs. d", "b vs. c", "b vs. d", "c vs. d" Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/l

[R] how to compute uncentered (pearson correlation) correlation efficiently

Hi, Seeking suggestions to compute uncentered (pearson correlation) correlation efficiently. corr from stats library works on x and y columns. dist from amap library works on x and y rows. My data layout is slightly different such that row(i) of matrix x is compared to row(i) of matrix y. Than

[R] queries about bitmap()

Hi, There are different types of tiff methods in bitmap(), which one should be used for publication-quality pictures ? '"tiffcrle"', '"tiffg3"', '"tiffg32d"', '"tiffg4"', '"tifflzw"', '"tiffpack"', '"tiff12nc"', '"tiff24nc"', Thanks [[alternative HTML version deleted]]

[R] questions about p.adjust

Hi, I have some questions about p.adjust. "The false discovery rate is a less stringent condition than the family wise error rate, so these methods are more powerful than the others.", these methods refer to FDR methods or FWER methods. Simply what are the differences/pros/cons of both classes of

Re: [R] unable to start device PNG and unable to open connection to X11 display

Hi, I consulted ?png, and it uses X11. is there any way to save plots into png, without using X11 ? On 3/3/08, Prof Brian Ripley <[EMAIL PROTECTED]> wrote: > > Please consult the help page for png. > > On Mon, 3 Mar 2008, Ng Stanley wrote: > > > Hi, > > > >

[R] unable to start device PNG and unable to open connection to X11 display

Hi, I have installed R on a computational cluster, and am using putty to access R. Please help on how to solve the problem of saving png files. > png(file="myplot.png", bg="transparent") Error in X11(paste("png::", filename, sep = ""), width, height, pointsize, : unable to start device PN

[R] Grouping 30 arrays (geographical) of 1000 rows (individuals) by 20 columns (time-series data)

Hi, I have 30 arrays (geographical) of 1000 rows (individuals) by 20 columns (time-series data), and need to group arrays that are most similar. What packages and functions will be useful for this task ? Thanks Stanley [[alternative HTML version deleted]] __

[R] problem with heatmap.2

Hi, > temp1[1:6,] _XXX BB_XXX C_XXX D_XXX E_XXX SkHep1_XXX 500.75285 0.30630 0.56330 0.45755 0.496650.74685 630.35930-0.22725 0.04725 0.53955 0.563900.51170 69 -1.57515-1.67610 -1.61695 -1.11685 -0.00085 -1.89155 910.84640 0.43

[R] How to check cy5 and cy3 values were lowess normalized

Hi, I have some microarray data, cy5 and cy3 values are in log2. Is there a way to check they have undergone lowess normalization ? Thanks Stanley [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/

[R] R equivalent of linux "cut", "paste", and "grep" ?

Hi, What functions should I use in order to perform the following steps: 1) Load a particular column (e.g., column 5) from a csv file 2) Append the column 5 to another csv file 3) select those rows that match specific keywords in column 5 [[alternative HTML version deleted]] ___

[R] indices of rows containing one or more elements >0

Hi, Given test <- matrix(c(0,2,0,1,3,5), 3,2) > test[test>0] [1] 2 1 3 5 These are values >0 > which(test>0) [1] 2 4 5 6 These are array indices of those values >0 > which(apply(test>0, 1, all)) [1] 2 This gives the row whose elements are all >0 I can't seem to get indices of rows containin

Re: [R] How to make t.test handle "NA" and "essentially constant values" ?

I met with a problem. The previous post dealt with loop, but mine is used in apply(). Please help. On 2/12/08, Ng Stanley <[EMAIL PROTECTED]> wrote: > > Thanks, that problem looks very similar to mine. try is a nice hack. I was > thinking t.test would be intelligent enough to disp

Re: [R] How to make t.test handle "NA" and "essentially constant values" ?

you're doing many t-tests > in a loop? If so there was a post very recently on this list about this: > > https://stat.ethz.ch/pipermail/r-help/2008-February/153254.html > > Richard. > > > Ng Stanley wrote: > > Thanks. Someone please help to make t.test go through al

Re: [R] How to make t.test handle "NA" and "essentially constant values" ?

Thanks. Someone please help to make t.test go through all the data and not to be disrupted by the two problems. On 2/12/08, Petr PIKAL <[EMAIL PROTECTED]> wrote: > > Hi > > [EMAIL PROTECTED] napsal dne 12.02.2008 09:09:23: > > > Hi, > > > > First problem: > > > test <- matrix(c(1,1,2,1), 2,2) > >

[R] How to make t.test handle "NA" and "essentially constant values" ?

Hi, First problem: > test <- matrix(c(1,1,2,1), 2,2) > apply(test, 1, function(x) { t.test(x) $p.value }) Error in t.test.default(x) : data are essentially constant Second problem: > test <- matrix(c(1,0,NA,1), 2,2) > apply(test, 1, function(x) { t.test(x) $p.value }) Error in t.test.default(x) :

[R] Conditional rows

Hi, Given a simple example, test <- matrix(c(0.1, 0.2, 0.1, 0.2, 0.1, 0.1, 0.3, 0.1, 0.1), 3, 3) How to generate row indexes for which their corresponding row values are less than or equal to 0.2 ? For this example, row 2 and 3 are the correct ones. Thanks [[alternative HTML version de

Re: [R] error message from apply()

4871174, 0.9450363, 0.4797723, -0.9033313, - > + 0.5825065, 0.8523742, 0.7402795, -0.7134312, -0.8162558, 0.6345438, - > + 0.05704138), 3,10) > > > > num <- apply(data2_1, 2, function(x) {sum(x > (mean(x, na.rm = TRUE) + > + 1*sd(x, na.rm = TRUE)), na.rm = TRUE)}) > > num >

[R] error message from apply()

Hi, I keep getting the error message. Please help. Error in colMeans(x, na.rm = TRUE) : 'x' must be an array of at least two dimensions The codes are: data2_1 <- matrix(c(0.9584190, 0.2710325, -0.9495618, -0.1301772, -0.7539687, 0.5344464, -0.8205933, 0.1581723, -0.5351588, 0.04448065, 0.9936

[R] How to generate table output of t-test

Hi, Given test <- matrix(c(1, 1,2,2), 2,2) t <- apply(test, 1, t.test) How can I obtain a table of p-values, confidence interval etc, instead of [[1]] One Sample t-test data: newX[, i] t = 3, df = 1, p-value = 0.2048 alternative hypothesis: true mean is not equal to 0 95 percent con

[R] Warnings from apply "longer object length is not a multiple of shorter object length"

Hi, What was I doing wrong, such that B) gave warning messages ? I want the computation of thr to be outside the apply function. A) Uses a simple matrix of 9 elements. No warning messages. data2_1 <- matrix (c(1,2,3,NA,4,5,NA,NA,6), 3,3) mean <- colMeans(data2_1, na.rm = TRUE) sd <- sd(data2_1,

[R] counts of each column that are not NA, and/or greater than column means

Hi, Given a test matrix, test <- matrix(c(1,2,3,NA,2,3,NA,NA,2), 3,3) A) How to compute the counts of each column (excluding the NA) i.e., 3, 2, 1 B) How to compute the counts of each column (excluding the NA) that are greater than the column means ? i.e., 1, 1, 0 I could write a for loop, but

[R] problem getting multiple densityplots on one page

Hi, I used the following statements to generate unsuccessfully a 5 by 5 multiple densityplots on a single page. If I use plot, the whole thing works. > data <- matrix(rnorm(25), 5, 5) > op <- par(mfrow = c(5, 5)) > for (x in 1:5) {densityplot(data[,x])} > par(op) Thanks Stanley [[altern

[R] Cannot save histogram picture when run from script

Hi, I am faced with a strange problem. My picture file is empty when the following statements were run from R script. But the picture file shows up correctly, when the commands are individually run from Rgui. png(file="histogram_correlation.png", bg = "white") require(stats) histogram( ~ height |

[R] permutates and/or samples a matrix

Hi, sample(x) only permutates and/or samples from a vector, which I can't use for a matrix. Please help. Thanks Stanley [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEA

Re: [R] Bug with hist() ?

My bad. Confused density with %. On Jan 31, 2008 7:50 PM, Martin Maechler <[EMAIL PROTECTED]> wrote: > >>>>> "NS" == Ng Stanley <[EMAIL PROTECTED]> > >>>>> on Thu, 31 Jan 2008 16:56:26 +0800 writes: > >NS> Hi, >

[R] Bug with hist() ?

Hi, Is this a bug from hist() ? The total density is greater than 1. > test [1] 0.05077802 -0.50585520 -0.98053648 -0.35513059 0.86767129 0.61736097 [7] 0.14264062 0.26243841 -0.41477782 0.64172618 0.87230953 -0.62570629 [13] 0.43596467 -0.93214106 -0.26781599 > h <- hist(test, freq =

[R] heatmap and legend

Hi, This should be elementary, but I can't find any resource on creating a legend for heatmap. Please help. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read th

[R] add/subtract matrices, ignoring NA or missing values

Hi, For example, given two 2x2 matrices m1 and m2. I would like to add/subtract element by element > m1 [,1] [,2] [1,] NA NA [2,]12 > m2 [,1] [,2] [1,]1 NA [2,] NA2 > m1 + m2 [,1] [,2] [1,] NA NA [2,] NA4 How can I ignore the NA, and g