similar to: Unable to execute lm function within a Rscript launch in the Linux Terminal

Hi, I cant understand where I am going wrong.Below is my code.I would really appreciate your help. Thanks. > genfile<-read.table("c:/tina/phd/bs871/hw/genfile.txt",skip=1) > > #read in SNP data > snp.dat <- as.matrix(genfile) > snp.name <- scan("c:/tina/phd/bs871/hw/genfile.txt",nline=1,what="character") Read 100 items

Hello everyone, This should be an easy question, I think. I'd like to write a command in a program to set the working directory to whatever directory the file is currently stored in. Suppose I have a file called "myRscript.r", and it's stored in "C:\Rprojects\myRscript.r", and it references other R scripts and data files in the same directory. If I enter the

Hi there, I am trying to find an example how to use Rscript Let's suppose I want to pass 3 arguments (I don't want [options] and -e [expressions] as described in help) *on the command line myRscript.R -arg1=value1 -arg2=value2 -arg3=value3 *In the script #! /path/to/Rscript args = commandArgs(TRUE); >From what I see args is just a string, do I do things correctly ? -- View this

Hello, All, GWAF 1.2 R.Version() is below. system(lme.batch.imputed( phenfile = 'phenfile.csv', genfile = 'CARe_imputed_release.0.fhsR.gz', pedfile='pedfile.csv', phen='phen1', covar=c('covar1','covar2'), kinmat='imputed_fhs.kinship.RData', outfile='imputed.FHS.IBC.GWAF.LME.output.0.txt' )) Gives the error messages: Error in

I had some problem when I compiled openssh-1.2.2 on FreeBSD 3.3 with enable skey option like this: ./configure --with-tcp-wrappers --with-skey .. .... ...... gcc -o sshd sshd.o auth-rhosts.o auth-krb4.o auth-pam.o auth-passwd.o auth-rsa.o auth-rh-rsa.o pty.o log-server.o login.o servconf.o serverloop.o bsd-login.o md5crypt.o -L. -L/usr/local/ssl/lib -lssh -lz -lcrypto -lutil -lpam -lskey -lwrap

Hi - I'm just starting out with R and have come up against a problem with what should be a simple operation. I'm plotting a range of safety standards for 7 different chemicals. I don't want the standard box and whisker plot - I just a dot for each value. Whilst using "plot.default" I get the error "invalid xlim value" - which is confusing since using the same script

Dear list, I'm running an R script which first line is: #!/usr/bin/Rscript While running that script from the system console (in Red Hat Enterprise Linux 6) I got the following error: Error in plot2(x = sim, y = obs, plot.type = "single", main = paste("Daily", : could not find function "hasArg" Calls: plot_results -> plot_out -> ggof -> plot2

Hi, I'm running Samba 2.0.4b on a Debian Linux (v2.2) PC. If I look at the "log.smb" file there are many messages: Attempt to locate null printername! Internal error? We have a number of print queues defined and they work fine. Here is a portion of the /etc/printcap: ================================================= # # Copyright (c) 1983 Regents of the University of California.

Hi all! I am using GenABEL on R for GWAS analysis. I am having a couple of issues: First, I am having a problem reading files (.map, & .ped, size 900Mb, using windows 32-bit) onto R in the "convert.snp.ped" statement. I am thinking this problem is likely due to the large size of the files & my version of R is not able to handle them, since I can read in smaller files.

Hello, I just created a little package, RcppProgress, to display a progress bar to monitor the execution status of a C++ code loop, possibly multihreaded with OpenMP. I also implemented the possibility to check for user interruption, using the work-around by Simon Urbanek. I just uploaded the package on my R-forge project, so you should be able to get the package from

Hi R-help folks, I have been doing some single SNP association work using snpMatrix. This works well, but produces a lot of false positives, because of population structure in my data. I would like to correct the p-values (which snpMatrix gives me) for population structure, possibly using principle component analysis (PCA). My data is complicated, so here's a simple example of what

Hi Peter, Rui, Chrstophe and Gabriel, Thanks for your inputs -- the use of qnorm(., log=TRUE) is a good point in line with pnorm with which we devised log(p) as log(2) + pnorm(-abs(z), lower.tail = TRUE, log.p = TRUE) that could do really really well for large z compared to Rmpfr. Maybe I am asking too much since z <-20000 >

Dear R gurus, I am interested in permutations-based cpu-intensive methods so I had to pay a little attention to Random Number Generators (RNG). For my needs, RNGs have to: 1) be fast. I profiled my algorithms, and for some the bottleneck was the RNG. 2) be scalable. Meaning that I want the RNG to remain fast as I add threads. 3) offer a long cycle length. Some basic generators have a

include/Rmath.h declares a set of 'logspace' functions for use at the C level. I don't think there are core R functions that call them. /* Compute the log of a sum or difference from logs of terms, i.e., * * log (exp (logx) + exp (logy)) * or log (exp (logx) - exp (logy)) * * without causing overflows or throwing away too much accuracy: */ double Rf_logspace_add(double

Hi All, Thanks for all your comments which allows me to appreciate more of these in Python and R. I just came across the matrixStats package, ## EXAMPLE #1 lx <- c(1000.01, 1000.02) y0 <- log(sum(exp(lx))) print(y0) ## Inf y1 <- logSumExp(lx) print(y1) ## 1000.708 and > ly <- lx*100000 > ly [1] 100001000 100002000 > y1 <- logSumExp(ly) > print(y1) [1] 100002000

I agree with many the sentiments about the wisdom of computing very small p-values (although the example below may win some kind of a prize: I've seen people talking about p-values of the order of 10^(-2000), but never 10^(-(10^8)) !). That said, there are a several tricks for getting more reasonable sums of very small probabilities. The first is to scale the p-values by dividing the

How can I delete both rows and columns that do not meet a particular cut off value. Example: > d <- rbind(c(0, 1, 6, 4), + c(2, 5, 7, 5), + c(3, 6, 1, 6), + c(4, 4, 4, 4)) > f <- as.matrix(d) > f [,1] [,2] [,3] [,4] [1,] 0 1 6 4 [2,] 2 5 7 5 [3,] 3 6 1 6 [4,] 4 4 4 4 I would like to delete all

I've hacked R so that it can be used to write shell and/or CGI scripts, e.g. "hello world" can be written as: #!/usr/local/lib/R/bin/R.bin --script cat("Hello, World!\n"); The mods required to enable this aren't particularly major. (Adds about 70 lines of code, IIRC.) Anyone else interested in adding this to the R core? -- Neil D. McKay, Mail Code 480-106-359

>>>>> William Dunlap via R-devel >>>>> on Sun, 23 Jun 2019 10:34:47 -0700 writes: >>>>> William Dunlap via R-devel >>>>> on Sun, 23 Jun 2019 10:34:47 -0700 writes: > include/Rmath.h declares a set of 'logspace' functions for use at the C > level. I don't think there are core R functions that call

You may want to look into using the log option to qnorm e.g., in round figures: > log(1e-300) [1] -690.7755 > qnorm(-691, log=TRUE) [1] -37.05315 > exp(37^2/2) [1] 1.881797e+297 > exp(-37^2/2) [1] 5.314068e-298 Notice that floating point representation cuts out at 1e+/-308 or so. If you want to go outside that range, you may need explicit manipulation of the log values. qnorm()