similar to: Re: QTL interval mapping in outbred populations

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,

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 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_trt.csv") --Read the following data: 75 individuals

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

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.

Hello R Power Users, There is a rather large introduction you may skip to go directly to my question about S4 classes. I am working on some toy code to help me get in through S4 classes. Doing this homework, I have some questions about S4 classes. I have carefully read available help and some additional material such as Robert Gentleman's slides and special attention to "Programming

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 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

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

It looks like a homework assignment. It also looks like you didn't read the documentation carefully enough. The 'len.out' argument in seq is solely for specifying the length of a sequence. The 'quantile' function omputes the empirical quantile of raw data in the vector 'x' at cumulative probabilit(y)(ies) given in the weights' argument, with interpolation I'm

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

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,

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", +

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) >

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