similar to: R/qtl

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

On Mon, 8 Nov 2004 ssim at lic.co.nz wrote: > > Is there an add-on package in R for QTL interval mapping for outbred > population, eg. Haley-Knott regression method ? > > Stella I believe Karl Broman's R/QTL (http://biosun01.biostat.jhsph.edu/~kbroman/software/) and Brian Yandell's bim (http://www.stat.wisc.edu/~yandell/qtl/software/), Richard Mott's happyR

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

Dear R-help We have a regression problem which could be solved elegantly if we could figure out how to get the R residuals() function to accept missing dependent variables. We have ~20000 gene-expression vectors y, each being measured on the same set of individuals, but each having a small random number of missing values. For each expression vector we wish to search across the genome

Hi, If you have multiple players installed on your PC/Mac .m3u will always open the last media player who are the default in charge of the extension and mime m3u. On your web site you want maybe to force a link to open real media player or quicktime/itune. You need to create a .pls to force winamp loading the streaming because windows media player won't open .pls etc. If you add a .pls

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 lists, Is there an add-on package in R for QTL interval mapping for outbred population, eg. Haley-Knott regression method ? Tanx Stella ___________________________________________________________________________ This message, including attachments, is confidential. If you are not the intended recipient, please contact us as soon as possible and then destroy the message. Do not copy,

Hi the list, A new version (0.92) of my package 'noia' will be available soon on CRAN mirrors, and I think it might be a good opportunity to introduce it shortly to the R community. In summary: 'noia' will be of absolutely no interest for 99.99% of you. The 0.01% remaining are quantitative geneticists who are interested in measuring the effect of genes in a proper way. Since

Hi the list, A new version (0.92) of my package 'noia' will be available soon on CRAN mirrors, and I think it might be a good opportunity to introduce it shortly to the R community. In summary: 'noia' will be of absolutely no interest for 99.99% of you. The 0.01% remaining are quantitative geneticists who are interested in measuring the effect of genes in a proper way. Since

Dear R community, I need to plot the results of some simulations I did using QTL Cartographer. I am plotting LOD scores over three chromosomes. The three plot have to be one next to the other. The procedure I am using is: par(mfrow=c(1,3)) plot(x$x, x$y, ylim=c(0,35), type="l", col="blue", las=1, xaxs="i", yaxs="i", xlab="X Chromosome",

Bottom Line Up Front: How does one reshape genetic data from long to wide? I currently have a lot of data. About 180 individuals (some probands/patients, some parents, rare siblings) and SNP data from 6000 loci on each. The standard formats seem to be something along the lines of Famid, pid, fatid, motid, affected, sex, locus1Allele1, locus1Allele2, locus2Allele1, locus2Allele2, etc In other

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

Infomaniak Network SA / Guy Baconniere wrote: > Hi Karl, > >> While I think most of this is fine, I think in the fserve part (where >> the checks to see if there is a playlist file in webroot), they all >> seem to follow the same pattern so that would tend to indicate a >> function to reduce duplication. >> >> At the moment I'm wondering whether these

Hi Karl, > While I think most of this is fine, I think in the fserve part (where > the checks to see if there is a playlist file in webroot), they all > seem to follow the same pattern so that would tend to indicate a > function to reduce duplication. > > At the moment I'm wondering whether these responses could be > automatically generated from xslt files? like xspf is.

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

Hi all, This is really a stats question as much as an R question. I'm trying to do a joint scaling test (JST - see below) on some very oddly-distributed data and was wondering if anyone can suggest a good way of dealing with model violations and/or using R to evaluate how sensitive the model is to violations of the normality assumption. Here's a quick explanation of the analysis, the

Hello R-users! I have a style question. I know that for loops are somewhat frowned upon in R, and I was trying to figure out a nice way to do something without using loops, but figured that i could get it done quickly using them. I am now looking to see what kind of tricks I can use to make this code a bit more aesthetically appealing to other R users (and learn something about R along the

Hi, For the last few days I have tried utilise your package "pegas" in order to obtain some values for indices like the nuclear diversity and tajimas d value. I have modified my dataset (a text file containing dna sequences) in order to be able to read it in with the tools provided by pegas. Here, I have oriented myself on the description provided by the help-page in read.loci().

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