similar to: Getting rid of for loops

Dear R users The following question looks simple but I have spend alot of time to solve it. I would highly appeciate your help. I have following dataset from family dataset : Here we have individuals and their two parents and their marker scores (marker1, marker2,....and so on). 0 means that their parent information not available. Individual Parent1 Parent2 mark1 mark2 1 0 0

Dear all, I would like to know if it is possible to fit in R a Cox ph model with time-dependent covariates and to account for hierarchical effects at the same time. Additionally, I'd like also to know if it would be possible to perform any feature selection on this model fit. I have a data set that is composed by multiple marker measurements (and hundreds of covariates) at different time

R-devotees, I have a question about modeling in the case where the response variable is binary. I have a case where I have a response variable that is the probability of success, and four descriptor variables, The response has a sigmoid response with one of the variables. I would like to test for the effect of the various descriptor variables on the percentage success of the binary trait. I have

Hi everybody!! I'm trying to assign boolean values to a column in a matrix depending on the number of times present in another column. I have no clue, I have been 2 days looking for a way, if somebody knows what kind of functions I need to use I will really apreciate it. example: Color Type Mark1 Mark2 Mark3 Red high 139 P alpha blue low 140 P alpha Green high

Hello R-helpers! I have a question concerning extracting sequence information from a vector. I have a vector (representing the bins of a time series where the frequency of occurrences is greater than some threshold) where I would like to extract the min, median and max of each group of consecutive numbers. For Example: tmp <- c(24,25,29,35,36,37,38,39,40,41,42,43,44,45,46,47,68,69,70,71) I

Could you help me in getting a package to compile from source in Windows? I'm running Windows NT 4.0 on a pentium 450 with 128 Mb of Ram. I've got R 1.0.0. I am developing a package for R which includes a bit of C code. I have things working in Unix just fine, and now I want to port it to Windows NT. I've been following the instructions in the R complements to Venables and

Dear R-Helpers, I am using qtl package to analyze qtl data from QTL cartographer. I have the map file and cro file from QTL cartographer. I was trying to import these two files in R using qtl package. data=read.cross("qtlcart", ".", "crofile.txt", "mapfile.txt") ### I have matched the file structure with the one on the website of qtl package - It matches

Hi R, I tried to install one local source package---"qtl" into R, but failed with the following message. I am using Macbook OS 10.8.3 with Xcode 4.6.1. ld: warning: directory not found for option '-L/usr/local/lib' ld: library not found for -lgfortran collect2: ld returned 1 exit status make: *** [qtl.so] Error 1 ERROR: compilation failed for package ¡®qtl¡¯ * removing

Hello... I tried to compile an R addon package, R/qtl on a Solaris machine and I get this error. I know that R/qtl complies correctly on other platforms (Windows, Mac, Linuxes, etc), so I am wondering what the problem might be. Any ideas? Thanks, Saunak ----------------------------------- /export/home/sen/tmp <howrahbridge> <pts/5> R INSTALL

---------- Forwarded message ---------- From: Waqas Shafqat <waqas1518@gmail.com> Date: Fri, Sep 6, 2013 at 10:31 PM Subject: To: rosyara@msu.edu sorry sir i have istalled plantbreeding libraray..but when i give command "require(plantbreeding)" then following message appear > require(plantbreeding) Loading required package: plantbreeding Loading required package: qtl Failed

Hello... I just installed R version 1.4.0 on my laptop running Redhat Linux 7.1. I downloaded the RPM from CRAN and when I try to use a function I have used on other Redhat systems, I get the following error message. -------- > library(qtl) > gastritis <- read.cross(format="csv",dir="/home/sen/qtl/data/gastritis", +

Hello, I have a bar plot where I am already using colour to distinguish one set of samples from another. I would also like to highlight a few of these bars as ones that should be looked at in detail. I was thinking of using hatching, but I can't work out how or if you can have a background colour and hatching which is different between bars. Any suggestions on how I should do this? Thanks

Sorry: resending this; didn't have a title on it. Trying to set up multiple spawns of R ------------------------------------------- Hi. I'm new to the list but I have a small problem with R. I'm trying to set up multiple spawns of R active at the same time on an AMD with a dual core in Vista so that I can cut down my permutation processing time. I've installed R in multiple

Hi, I'm using R for a QTL analysis of SNP data. I was wondering if anyone had any advice on fitting a dominance effect into the following function; > myfun4 function (x) { x <- scan(con, nmax=169) y <- unique(x[which(!is.na(x))]) if(length(y)>1) { summary(lme(Ad ~ x, random= ~1|sire, na.action="na.omit")) } else {print("no.infomation")} } Con is the

Dear UseR, I get an error when I run "R CMD check" on my .tar.gz file package, and I don't understand why since I don't obtain any error with "R CMD check" on the package directory. Do you have any idea ? $ sudo ./R-2.11.0/bin/R CMD check eqtl_1.1.tar.gz and $ sudo ./R-2.11.0/bin/R CMD --check-subdirs=no eqtl_1.1.tar.gz return an Error * checking for working

Hello, I'm trying to get the count of values in each row that are above and below quantile thresholds. Thanks! Example: > x = matrix(1:30,5,6) > x [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 6 11 16 21 26 [2,] 2 7 12 17 22 27 [3,] 3 8 13 18 23 28 [4,] 4 9 14 19 24 29 [5,] 5 10 15 20 25 30 > qtl = t(apply(x, 1,

R-masters, I have a problem that I have been working on for a while and it seems that there may be a simple solution that I have yet to figure out, so I thought that I would venture to post to the help list. Let's say there was a data.frame with three vectors, two that are factors identifying the data, and one that holds the frequency of occurrence (the events are binary, yes or no). I

Hi I made heatmap of QTL based on Lod score. Where I have traits in columns and marker data (rows). I can not cluster both column and rows as I need the right order for marker data. Can someone suggest me better way of generating heatmaps especially the colour key I want to select to visualize the results which are more interesting to look at. > library(gplots) >

I want to specify a two-factor model in lme, which should be easy? Here's what I have: factor 1 - treatment FIXED (two levels) factor 2 - genotype RANDOM (160 genotypes in total) I need a model that tells me whether the treatment, genotype and interaction terms are significant. I have been reading 'Mixed effects models in S' but in all examples the random factor is not in the main

Dear R users,   I am trying to use "wgaim" package for QTL analysis using mixed model approach. But i am stuck with "asreml" function while using "wgaim" package. Do i need a separate package to activate "asreml" function beside "wgaim" package ?   If so, i tried to download "Asreml-R" package (i guess this is right package