search for: qtl

...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 Ripley's book, "Building from a source-code library under Windows." I installed cygwin-20 and gcc-2.95.2, and ran "make pkg-qtl" (qtl is the name of the package). That part works just fine. But then when I run "make pkgcheck-qtl" I get the following error. ====================================================================== bash-2.02$ make pkgcheck-qtl -------- Testing package qtl -------- Running exam...

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 fi...

...ks I can use to make this code a bit more aesthetically appealing to other R users (and learn something about R along the way...). Here's the problem. I have a data.frame with 4 columns of dependent variables and then ~35 columns of predictor variables (factors) [for those interested, it is a qtl problem, where the predictors are genotypes at DNA markers and the dependent variable is a biological trait]. I want to go through all pairwise combinations of predictor variables and perform an anova with two predictors and their interaction on a given dependent variable. I then want to store th...

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 (http...

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>...

...te: 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 with error: ‘package ‘qtl’ could not be loaded’ In addition: Warning message: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called ‘qtl’ further any anlysis i.e dialle or stability not to be done please guide me sorry to disturb...

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 f...

Dear all, I am running qtl mapping. I have 75 RI lines with some residual heterogeneous loci. The loci are code A, B or H(heterogeneous). Questions: 1) R/qtl determine the data is F2 intercross. 2) Warning message about strange genotype pattern > library(qtl) > dat=read.cross("csv", file="rqtl_tr...

...can cut down my permutation processing time. I've installed R in multiple places, which I thought was the correct way to do it but whether I use installs at "C:\Program Files\R1" and "C\...\R2", or even separately on the C: and D: drive, whenever I try to load my package (qtl), it gives me the error message: Error in library(qtl) : there is no package called 'qtl' The thing is, I've installed the packagen in both places (C\...\R1 and C\...\R2, or both the C: and D: drives) and it still gives me the message. Does anyone know how to set up a simultaneous R...

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&quo...

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 a...

...rve.c, + trunk/icecast/web/status.xsl, trunk/icecast/web/auth.xsl, + trunk/icecast/admin/listmounts.xsl, trunk/icecast/admin/stats.xsl, + trunk/icecast/admin/listclients.xsl, + trunk/icecast/doc/icecast2_basicsetup.html, + trunk/icecast/doc/icecast2_listenerauth.html: + add pls,asx,ram,qtl support when user want to launch a specific player + Now support winamp, windows media player, real media player, quicktime player + listing format. + 2005-11-29 03:06 karl * trunk/icecast/src/auth_url.c: update for authentication header --- admin/listclients.xsl 2005-09-27 22:22:18.00000...

Hi folks, OS - Ubuntu 10.04 On R I create a datafile named "data". I can evoke it on R with; > data On R Commander Data -> Active data set -> Select active data set -> (data) OK only one data set there "data" -> View data set I can read it -> Edit data set showing 25 rows of data. Clicking the box shows a thick border around it. But I couldn't

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.

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 pdflatex ... OK * using log directory '/home/hkhalili/Desktop/eqtl.Rcheck' * using R version 2.11.0 (2010-04-22) * using session charset: UTF-8 * checking for file 'e...

...e may be a canned function in R but you can always write your own. First we write one that takes values in 'x' and weights in 'w', vectors of the same length, and returns the quantile at cumulative probability 'p' for a 'p' of length 1. "%,%" <-paste0 qtl.one <- function(p, x, w) { ## argument checking bad <- length(x)!=length(w) bad <- bad || (length(p)!=1) bad <- bad || any(diff(x)<=0) if(bad) stop("Arguments 'x' and 'w' must be " %,% "vectors of the same legnth. Argumen...

...e 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, quantile, probs = c(.1,.9),na.rm=T)) > qtl 10% 90% [1,] 3.5 23.5 [2,] 4.5 24.5 [3,] 5.5 25.5 [4,] 6.5 26.5 [5,] 7.5 27.5 I would like counts like this for each row: cnts [,1] [,2] [1,] 1 1 [2,] 1 1 [3,] 1 1 [4,] 1 1 [5,] 1 1 ...because for th...

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", + "Pablodata.csv",genotypes=c("b","h","c")) stack imbalance in internal type.convert, 48 then 47stack imbalance in .Internal, 47 then 46 st...

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...