Grokbase Groups R r-help July 2011

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859 discussions - 2,915 posts

  • Dear all, I am doing a project on variant calling using R.I am working on pileup file.There are 10 columns in my data frame and I want to count the number of A,C,G and T in each row for column ...
    Bansal, VikasBansal, Vikas
    Jul 1, 2011 at 4:47 pm
    Jul 5, 2011 at 4:16 pm
  • Dear R users, I have a desktop computer and a laptop, both of them with Ubuntu Lucid. The former has R2.10 installed from Ubuntu repositories (this is the most recent version in the repositories), ...
    Jul 21, 2011 at 7:23 am
    Aug 30, 2011 at 12:02 pm
  • Hello! It's a shoot in the dark, but I'll try. If one has a total of 100 (e.g., %), and three components of the total, e.g., mytotalÚta.frame(xP,y0,z ), - one could build a pie chart with 3 sectors ...
    Dimitri LiakhovitskiDimitri Liakhovitski
    Jul 21, 2011 at 3:29 pm
    Jul 26, 2011 at 12:49 pm
  • I created this graph in ggplot and added ablines to the different facets by specifying with subset commands. As you might see, there are still a few issues. 1.) I would like to have the diamonds in a ...
    Jul 10, 2011 at 3:24 am
    Jul 28, 2011 at 10:44 pm
  • Hello I am new to R and I need to convert some dates (numeric format by matlab) to actual dates in R. For instance, Matlab - 730456 - datestr(730456) ans = 02-Dec-1999 R - [1] "3969-12-03" I don't ...
    Eduardo M. A. M. MendesEduardo M. A. M. Mendes
    Jul 17, 2011 at 3:50 am
    Jul 20, 2011 at 11:46 am
  • Dear R folks, I need to simulate first passage times for iterated partial sums. The related papers are for example [1][2]. As a start I want to simulate how long a simple random walk stays negative, ...
    Paul MenzelPaul Menzel
    Jul 27, 2011 at 11:36 pm
    Aug 2, 2011 at 11:41 am
  • Using str() in a function. I am in the early phase of learning R, and I find I spend a lot of time trying to figure out what is actually in objects I have created or read in from a file. I'm trying ...
    Jul 9, 2011 at 8:20 am
    Jul 15, 2011 at 6:06 pm
  • Hi, I am trying to do a simple multiple regression analysis that has one nominal variable (gender) and three numeric variables as independent variables and one numeric variable as dependent ...
    Jul 19, 2011 at 9:39 pm
    Jul 21, 2011 at 2:47 pm
  • HI All, I have written and succesfully uploaded a new package. The licence it is under is 'GPL' --no version. My assumption is, since all the code is written in R the licence R used for R would ...
    Federico CalboliFederico Calboli
    Jul 8, 2011 at 10:20 am
    Jul 9, 2011 at 8:41 am
  • Hi May you help me correct my loop function. I want optim to estimates al_j; au_j; sigma_j; b_j by looking at 0 to 20, 21 to 40, 41 to 60 data points. The final result should have 4 columns of each ...
    Jul 4, 2011 at 9:34 am
    Jul 8, 2011 at 6:04 am
  • I am looking for a way to save a plot (graphics contents) to a file after the plot has been calculated but before it has been rendered. More specifically, assume that I made a plot that took a very ...
    Jul 11, 2011 at 4:08 pm
    Aug 1, 2011 at 10:47 am
  • Can someone help me out with a "small" problem? I've started using netcdf files recently, and I want to extract the grid id and also the coordinates from a HIRHAM netcdf file. I know how to extract a ...
    Jul 29, 2011 at 2:44 pm
    Jul 29, 2011 at 3:40 pm
  • I have tried a lot of ways around this, but I can't find a way to make apply work in a generalized way because it causes a failure whenever reduces the dimensions of its output. The following example ...
    Gene LeynesGene Leynes
    Jul 27, 2011 at 10:22 pm
    Jul 29, 2011 at 3:39 am
  • Dear all, I have one problem and did not find any solution.(I have also attached the problem in text file because sometimes column spacing is not good in mail) I have a file(file.txt) attached with ...
    Bansal, VikasBansal, Vikas
    Jul 14, 2011 at 3:35 pm
    Jul 15, 2011 at 9:29 pm
  • Hello! I am aggregating using a formula in aggregate - of the type: aggregate(cbind(var1,var2,var3)~factor1+factor2,sum,data=mydata) However, I actually have an object (vector of my variables to be ...
    Dimitri LiakhovitskiDimitri Liakhovitski
    Jul 14, 2011 at 7:05 pm
    Jul 15, 2011 at 1:23 pm
  • Hi, Am using R 2.13.1 on Linux (Fedora). Is anybody else having problems with dev.copy2pdf xyplot output with the pch=1 (open circle) symbol? The symbols come out as "q" in the PDF. dev.copy2eps ...
    Selwyn quanSelwyn quan
    Jul 28, 2011 at 5:22 pm
    Jul 30, 2011 at 5:07 pm
  • Hi all, I have R installed on a box, which is running on a machine with 16 core and Redhat - Linux. I am handling huge (size of dataset will be 5 GB) dataset. Lets assume that my data is in the form ...
    Jul 20, 2011 at 11:44 pm
    Jul 27, 2011 at 5:48 pm
  • Hi, If i want to repeat a function, say 100 times, how do i do that? i used the for loop but there's an error somewhere. Thanks shan
    Shantal BonnickShantal Bonnick
    Jul 2, 2011 at 1:03 pm
    Jul 26, 2011 at 3:41 pm
  • Dear sir, I am struggling with a problem.Please help me. Now I have a dataframe with these columns- V7 V8 V9 V10 0 1 G 82 0 1 CGT c(90, 92, 96) 0 1 GA c(78, 92) 0 1 GAG c(90, 92, 92) 0 1 G 88 0 1 A ...
    Bansal, VikasBansal, Vikas
    Jul 8, 2011 at 8:15 pm
    Jul 9, 2011 at 8:55 pm
  • Dear R folks, currently the section Examples contains the following as an example on how to plot a ?normal? function. plot(sin, -pi, 2*pi) Since it does not contain the argument for the function it ...
    Paul MenzelPaul Menzel
    Jul 27, 2011 at 7:30 pm
    Jul 29, 2011 at 8:54 am
  • Dear all, I am using the following function so that user can input a numerical value. readnumber<- function() { for(j in 1:10){ value=readline("enter the threshold for number of reads: ") ...
    Bansal, VikasBansal, Vikas
    Jul 25, 2011 at 2:59 am
    Jul 25, 2011 at 12:52 pm
  • Hi there, I have a large amino acid csv file like this: input.txt: P,LV,Q,Z P,VL,Q,Z P,ML,QL,Z There is a problem with this file, since LV and VL are in fact the same thing. How do I order each ...
    Jul 15, 2011 at 1:18 am
    Jul 15, 2011 at 11:27 am
  • Dear List, I have encountered an odd problem that I cannot understand. It stems from the calculation of true and false positives based on two input vectors x and y based on different thresholds of x, ...
    Lyndon EstesLyndon Estes
    Jul 11, 2011 at 8:57 pm
    Jul 14, 2011 at 2:29 am
  • Dear all, sorry if this is a bit on the sidetrack for R-help. As a regular R user I have developed quite a lot of custom R functions, to the point of not always remembering what I have already ...
    Simon Chamaillé-JammesSimon Chamaillé-Jammes
    Jul 9, 2011 at 11:30 am
    Jul 12, 2011 at 9:59 pm
  • Dear colleagues, I have a series of newspaper articles in a text file, downloaded from a text file. They look as follows: Document 1 of 100 \n \n \n Newspaper Name \n \n Day Date I have a series of ...
    Simon KissSimon Kiss
    Jul 11, 2011 at 4:31 pm
    Jul 11, 2011 at 8:29 pm
  • Hi All, I need to give my R code to my client to use. I would like to protect the logic/algorithms that have been coded in R. This means that I would not like anyone to be able to read the code. I am ...
    Vaishali SadaphalVaishali Sadaphal
    Jul 4, 2011 at 7:47 am
    Jul 5, 2011 at 3:15 am
  • Hi, I'm running a tutorial ("Meta-analyses of data from two (or more) microarray data sets"), which use wgcna package. I have an error in the function modulePreservation (it is below). I'm using ...
    Raquel Martinez GarciaRaquel Martinez Garcia
    Jul 6, 2011 at 3:27 pm
    Aug 1, 2012 at 10:33 pm
  • Dear experts I installed Rgraphviz with the following command: source("") biocLite("Rgraphviz") But had a problem when I tried to load it. This says that ...
    Ram H. SharmaRam H. Sharma
    Jul 25, 2011 at 1:05 pm
    Jun 24, 2012 at 4:53 pm
  • Dear friends, does anyone know how I can run a zero truncated poisson regression using R (or even SPSS)? Dr. Iasonas Lamprianou Department of Social and Political Sciences University of Cyprus
    Iasonas LamprianouIasonas Lamprianou
    Jul 31, 2011 at 4:59 pm
    Aug 1, 2011 at 11:14 pm
  • [Env: Win XP] I've just upgraded from R 2.12.2 to R 2.13.1. As part of my upgrade process, I typically install some in-development packages from R-Forge that are not on cran. But for the first time, ...
    Michael FriendlyMichael Friendly
    Jul 31, 2011 at 3:26 pm
    Aug 1, 2011 at 8:44 am
  • Good morning to all, I am encountering a blocking issue when using the function 'breackpoints' from package 'strucchange'. *Context:* I use a data frame, 248 observations of 5 variables, no NA. I ...
    Michel LutzMichel Lutz
    Jul 29, 2011 at 7:37 am
    Jul 30, 2011 at 2:08 pm
  • Hi, I want to generate multiple sets of random numbers. The requirement is that: 1) each set have 3 random numbers; 2) the sum of the three number is always 1. how to do this? thank you, karena -- ...
    Jul 21, 2011 at 11:18 pm
    Jul 22, 2011 at 10:13 am
  • Hi - I would like to make to make a barplot of my data, but am having issues. An example of my data is: species net pair pounds type Cod Control 1 46 kept Little Skate Control 1 0 kept Summer ...
    Jul 15, 2011 at 8:11 pm
    Jul 20, 2011 at 11:27 am
  • Hi, I am using ecdf-function and want to use the ecdf()-data-points for nls() as data-parameter. nls() expects 'list' or 'environment' as a data-type, knots(ecdf(mydata)) gives me 'numeric'. What ...
    Jul 16, 2011 at 12:17 pm
    Jul 19, 2011 at 12:46 am
  • Hi i have the data in the following format: rent,100,1,common,674 pipe,200,0,usual,864 car,300,1,uncommon,392:jump,700,0,common,664 car,200,1,uncommon,864:snap,900,1,usual,746 ...
    Jul 14, 2011 at 10:47 pm
    Jul 18, 2011 at 10:22 am
  • Hi .. i am a beginner in R I have data in the format of date 04/27/11 04/27/11 04/30/11 04/30/11 05/03/11 05/03/11 05/04/11.... Now i want to plot the data something like this on x-axis.. ...
    Jul 13, 2011 at 10:56 pm
    Jul 14, 2011 at 7:16 pm
  • Hi, I am trying to do a lasso regression using the lars package with the following data (see attached): FastestTime WinPercentage PlacePercentage ShowPercentage BreakAverage FinishAverage ...
    Heiman, Thomas J.Heiman, Thomas J.
    Jul 12, 2011 at 1:50 pm
    Jul 12, 2011 at 4:12 pm
  • Dear R community! I am new to R and would be very grateful for any kind of help. I am a PhD student and need to fit a model to an electricity load profile of a household (curve with two peaks). I was ...
    Jul 28, 2011 at 9:05 am
    Sep 20, 2011 at 2:42 pm
  • Hi, I?m trying to move to ubuntu at all, but I don?t like R in Ubuntu because it runs in the terminal, so i can?t access directly to some options R gots in Windows. Is there any R can i install in ...
    Jul 29, 2011 at 8:03 am
    Jul 31, 2011 at 6:50 pm
  • Hi all: There's a question about glht function. My data:data_ori,which inclue CD4, GROUP,time. f_GROUP<-factor(data_ori$GROUP) f_GROUP is a factor of 3 levels(0,1,2,3) result <- lme(sqrt(CD4) ~ ...
    Lao MengLao Meng
    Jul 26, 2011 at 7:16 am
    Jul 28, 2011 at 1:57 am
  • Greetings, I've been struggling for some time with a problem concerning a big database that i have to deal with. I'll try to exemplify my problem since the database is really big. Suppose I have the ...
    Jul 26, 2011 at 5:13 am
    Jul 27, 2011 at 10:29 pm
  • Hello I need to run an r-file that works on Windows on MAC. The first lines of the file are: library(R.matlab) library(Rcompression) Somehow I cannot find where Rcompression is. Am I missing ...
    Eduardo M. A. M. MendesEduardo M. A. M. Mendes
    Jul 13, 2011 at 12:40 am
    Jul 25, 2011 at 1:16 pm
  • Dear All, I have a massive dataset from which I would like to draw a histogram. Any ideas on how to accomplish this? Thanks in advance, Paul
    Paul SmithPaul Smith
    Jul 15, 2011 at 11:21 am
    Jul 19, 2011 at 1:43 pm
  • Hi all, I have an interval (e.g [-3,3]) and a numeric vector z (-1.4,0.5,4.7). How can I test whether an element in z lies between between -3,3? I particularly need a TRUE/FALSE response. Thanks ...
    Manuel K.Manuel K.
    Jul 17, 2011 at 2:54 pm
    Jul 18, 2011 at 9:21 pm
  • Hello, I have few questions about recurring events. I would greatly appreciate it if anyone can assist me. I have data that consist of approx 1,100 Consecutive patients released from hospital after ...
    Jul 5, 2011 at 6:55 pm
    Jul 18, 2011 at 3:02 pm
  • Hello. Is there a package or functionality available somewhere which will allow for complex searches (such as what SQL can do) of collections of RData files? Search capability within a given RData ...
    Bhushan, VipulBhushan, Vipul
    Jul 15, 2011 at 2:29 pm
    Jul 16, 2011 at 11:16 am
  • Hi, all: I used two lines of very simple code to draw a sin curve. = 640, height = 480) Now, I added a specific line (red line in the picture at by ...
    JIA PeiJIA Pei
    Jul 13, 2011 at 5:22 pm
    Jul 15, 2011 at 1:30 am
  • Friends, Could anyone help me the script, how to read the more than 15 columns from the file. I have Excel sheet, of course can save into any readable format. Appreciate your help. Thanks. -- View ...
    Jul 13, 2011 at 8:23 am
    Jul 14, 2011 at 12:48 pm
  • Dear group, I am working on a rather big project where the output data frames have dimensions of 3000 x 15 or greater. We are using xlsx and xlsx2 to write the data.frames to Excel sheets. Since ...
    Jul 13, 2011 at 9:46 am
    Jul 13, 2011 at 4:12 pm
  • Hi, I need this plot: given: x,y - numerical vectors of length N plot xi vs mean(yj such that |xj - xi|<epsilon) (running mean?) alternatively, discretize X as if for histogram plotting and plot mean ...
    Sam SteingoldSam Steingold
    Jul 11, 2011 at 7:18 pm
    Jul 12, 2011 at 4:01 pm
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David Winsemius: 253 posts Joshua Wiley: 91 posts Uwe Ligges: 63 posts Dennis Murphy: 58 posts Bansal, Vikas: 50 posts Duncan Murdoch: 49 posts Bert Gunter: 45 posts Sarah Goslee: 43 posts Peter dalgaard: 40 posts Gabor Grothendieck: 36 posts Jim Holtman: 35 posts Daniel Malter: 32 posts Jim Lemon: 27 posts Peter Ehlers: 26 posts Prof Brian Ripley: 26 posts Ben Bolker: 25 posts Dieter Menne: 22 posts Dimitri Liakhovitski: 22 posts Rolf Turner: 22 posts William Dunlap: 21 posts
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