similar to: Character SNP data to binary MAF data

Hi I was wondering if there was a way to run system when there is e.g. a C program which is not totally command-line driven. That is, I have a C program which requires manual input of options into the shell during the run. I would like to run this program from R and as far as I have seen system() does not handle manual options (?). Is there thus a way to use these C programs anyway through R

Hi I have sent a previous email "Error in dyn.load()" for which, shame on me, I later found a partial answer. I have been trying to look into what I exactly need to include into Makevars and where it needs to be located and have not found a satisfying answer yet. Maybe the following questions are helpful for other people as well. Again, I am trying to include a C function tools.c into

Hi, I am aware that this question might be a basic one. I did browse the help and archives but I still haven't understood how to do the following: I run R locally and would like to read in data from a server for which there is a username and password. That is, how do I open a connection to a server with a password? Thanks, Hadassa -- Hadassa Brunschwig PhD Student Department of Statistics

Hi I would like to produce a red shading I figured the easiest way to do that would be to use rgb in the following way: a <- seq(0,0.9,by=0.1) redshade <- rgb(red=1,green=a, blue=a) However, I don't really know how to plot things using hexadecimal colors. I used a function which tries to find the closest color to the rgb shades but it didn't work very well. Any

Hi All, I've been having a little trouble with creating a loop that will run a a series of t.tests for inspection, Below is the code i've tried, and some checks i've looked at. I've used the get(paste()) idea as i was told previously that the use of the eval should try and be avoided. I've run a single syntax to check that my systax is correct and works without any problems

Hi R-Help! I am trying to use R2WinBUGS but I get the following error message in WinBUGS (and there must be something wrong with my R statement as I tried it directly in WinBUGS and it worked): display(log) check(C:/Documents and Settings/Daikon/Roche/pop_model.txt) model is syntactically correct data(C:/Documents and Settings/Daikon/Roche/data.txt) expected key word structure compile(7) ...(and

Hi, I know that with readlines you can start executing a code upon user input. What I would like to do is to have the ability to abort a code based on a new user input. E.g. when the user hits enter the code stops running. That is, I would periodically check for a user input and stop the code when the correct input was entered. Below is an example of a function which would run an endless loop

Hi R-Help! My question: I have lifetime/failure data of machines with different stress levels and i think an weibull/extreme value distribution would fit this data. So I did: model1 <- survreg(Surv(lfailure)~stress,data=steel,dist="extreme") (where lfailure=log(failure)) Now I would like to do a likelihood ratio test to test the hypothesis H0: location parameters of the

Hi R-Users! I fitted a negative binomial distribution to my count data using the function glm.nb() and obtained the calculated parameters theta (dispersion) and mu. I would like to simulate values from this negative binomial distribution. Looking at the function rnbinom() I was looking at the relationship between the two possible parametrizations of the negative binomial and found that for this

Hi There must have someone already posted this question but I still have not figured how I could do this: Say I have var.1 var.2 var.3 which are large matrices. I would like to do the following loop: for(i in 1:3){ # Pick var.i and do something with it } How can I tell R to do this? Thanks for any comments. Hadassa [[alternative HTML version deleted]]

Hi, I was wondering if there is a way to control the strip size in xyplot for example using the strip.default function. Or do I need to redraw the strips by myself? I would like to make the strip slimmer and I have reduced the font size using cex. However, I don't know how to change the size of the strip. Thanks for any tips. Hadassa [[alternative HTML version deleted]]

Hello everyone I have data grouped by subjects and i used the trellis plot to show the curve for each subject. I have another vector "a" which gives me the highest points the curves for each subjects can achieve ( the curve is exponential ). Now i want to draw a horizontal line, whose values are saved in "a", on each plot for each subject. Is there any possibility to do that?

Hi R-users! I am trying to create a what I call inflated array (maybe there is already some other name for that). It is an array that changes dinamically its dimensions, e.g. the higher the number of third dimensions, the more rows in the array. So for example the array could look like the following: , ,1 1 2 3 4 , , 2 5 6 7 8 9 10 11 12 , , 3 13 14 15 16 17 18 19 20 21 22 23 24 Has

Dear R users! I used lme to fit a mixed model with random intercept and spatial Gaussian correlation i.e. I fitted a model of the following form: Y = X*beta + error and error = U + W(t) + Z where U is the random intercept (normally distributed), W(t) the stationary Gaussian process and Z also a normally distributed (the residual) rv. Each of these three random variables have a variance which

Hi everyone! This must be a common question but I have not found an answer to it in the archives yet. I am producing four plots with par(mfrow=c(2,2)). The x-axis is the same for all of them but the y-axis is different. What I would like to do is to have a different range of the y-axis and different intervals between tick marks. BUT I would like to have the same number of tick marks and I would

Thanks to everyone who replied to my first problem. Here is the second one: Is the function "lme" (Mixed Model) also in a foreign library(shouldnt, as this is a basic statistical function)? I am trying to use lme in R and it replies that it couldnt find the function lme...weird... Thanks for replying!

Hello everyone I've got another question on Trellis plots. I plotted my fitted model with plot(augPred(fitted model)). According to the description of this method, one can use any optional argument which is passed down to the xyplot function for Trellis plots. Additionally to the trivial plot i would like to insert a horizontal line. I tried to do it with the argument panel= function (...)

Dear All, The following code extracts from NCBI very nice output for ONE allele of a SNP (often the allele with the second largest frequency - usually termed the minor allele). It gives an average minor allele frequency from all NCBI sources (which is what I want, except I'd like the addition of data for all the other alleles of one SNP) plus a table of minor allele frequencies from each

Could anyone help me to find the mathematical expression to calculate the monotonicity correlation coefficient between two variables? Thanks in advance. Luis Rivera. Universidad de Alcal?. -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or

I know that there are quite a few packages out that there for cluster analysis. The problem that I am facing is finding a package that will not incorporate all my samples into clusters but just the samples that fit a threshold (that I have not set yet and may need help finding the right level) for genotyping. It should be able to "no call" samples outside the clusters. It also needs to