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Hello useRs, I am trying to put my funcs in a package to avoid clutter in my workspace as the funcs are now in .Rprofile. All plain R code no compilations. Using win XP with a full cygwin install and R2.12 I first did package.skeleton("mypack",list="getdfv", namespace=T) # just a single func which created a folder with the required stuff in it. Calling R CMD build creates a

Dear All, I am trying to calculate the Hardy-Weinberg Equilibrium p-value for 42 SNPs. I am using the function HWE.exact from the package "genetics". In order not to do a lot of coding "by hand", I have a for loop that goes through each column (each column is one SNP) and gives me the p.value for HWE.exact. Unfortunately some SNP have reached fixation and HWE.exact requires a

Hi everyone, I'm using the function 'HWE.exact' of 'genetics' package to compute p-values of the HWE test. My data set consists of ~600 subjects (cases and controls) typed at ~ 10K SNP markers; the test is applied separately to cases and controls. The genotypes are stored in a list of 'genotype' objects, all.geno, and p-values are calculated inside the loop over all

Hi, I have a genotype data for both case and controls and would like to calculate the HW p-value. However, since the number of one genotype is 0, I got wired result. Would someone help me to figure it out? Or confirm it's right? Thanks a lot. ============ > library( "genetics" ) NOTE: THIS PACKAGE IS NOW OBSOLETE. The R-Genetics project has developed an set of enhanced

Hi, I am having trouble compiling package gap http://www.hgmp.mrc.ac.uk/~jzhao/r-progs.htm on Tiger. I have installed XcodeTools 2.1. The binary version of gap currently available on CRAN has some bug and is fixed in the latest version. The message I get from R is below. Any help is greatly appreciated. best regards, Kenny Ye tar: Read 1536 bytes from - * Installing *source* package

Hello! First of all I must appologize if this has been raised previously, but search provided by Robert King at the University of Newcastle seems to be down these days. Additionally let me know if such a question should be sent to R-help. I did a contribution to function hwe.hardy in package 'gap' during the weekend. That functions performs Hardy-Weinberg equilibrium test using MCMC. The

https://bugs.freedesktop.org/show_bug.cgi?id=102722 Bug ID: 102722 Summary: [regression] changing resolution hangs the display on Lenovo Thinkpad p51 Product: xorg Version: unspecified Hardware: x86-64 (AMD64) OS: Linux (All) Status: NEW Severity: critical Priority: medium

The "genetics" package for handling single-locus genetic data is now available on CRAN in both source and Windows binary formats. The purpose of this package is to make it easy to create and manipulate genetic information, and to facility use of this information in statistical models. The library includes classes and methods for creating, representing, and manipulating genotypes

The "genetics" package for handling single-locus genetic data is now available on CRAN in both source and Windows binary formats. The purpose of this package is to make it easy to create and manipulate genetic information, and to facility use of this information in statistical models. The library includes classes and methods for creating, representing, and manipulating genotypes

Hello all, I am interested in simulating 10,000 2 x 3 tables for SNPs data with the Hardy Weinberg formulation. Is there a quick way to do this? I am assuming that the minor allelle frequency is uniform in (0.05, 0.25). -- Thanks, Jim. [[alternative HTML version deleted]]

Hello, I am trying to simulate 10 relicates of 100-tables. Each table is a 2 x 3 and 80% pf the tables are true nulls and 20% are non-nulls. The nulls follow the Hardy Weinberg distribution (ratio) 1:2:1. I have the code below but the p-values are not what I am expecting. I want to use the Cochran Armitage trend test to get the p-values. num.reps=10 num.vars=1000 pi0 = 80 num.subjects = 100

Please keep replies on the mailing list. On Wed, Jan 17, 2018 at 05:43:14AM -0500, Donald Harter wrote: > I tried to build it from the ubuntu source rpm. It requires package > debhelper >=10 > What I have is > ii debhelper 9.20160115ubuntu3 > > I have the latest stable release so it requires an unstable release. > I could try to do

Hi, I've tried to compile 3.0.22 on HPUX 10.20 and get the following error msg: No options are used when running 'configure'. checking configure summary ERROR: No locking available. Running Samba would be unsafe configure: error: summary failure. Aborting config ****** The server details: [qhus029@HP-UX]>uname -a HP-UX qhus029 B.10.20 A 9000/898 1684683361 two-user license

I am trying to find the likelihood ratio for a 2 x3 table (actually SNP data). I do not want the log likelihood. Is this the correct R code for the following table? Row totals are fixed at 100 each (case control situation). aa Aa AA Total 10 20 70 100 20 40 50 100 30 60 120 So the row totals are fixed. Is this the correct code3? Likelihood.ratio =

My main dev machine died a well-deserved death a few weeks ago after six and a half years of faithful service, and refused to be re-animated. A substantial part of setting up its replacement is re-running a lot of R vignettes (mostly for timing to establish new performance baselines) - and also cleaning away some such vignettes generated in the past under different versions of R. So I noticed a

Hi again! I would just like to add that this surely must be a problem with network disks. As I reported yesterady in, https://stat.ethz.ch/pipermail/r-devel/2005-March/032431.html I have problems with installing packages on network drive (where I have R installed), marked N: > install.packages("gap") trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES'

Hello R users, I am writing a summary() for a custom class, and am to display the integers right justified, Say where x is the vector with integers, I am using the following: cat("\t",format(x),"\t"...other columns) this way I am trying to pass the format(x), to the cat function to display it, but still I am getting a kink(b/w the 9th and 10th row). 6 81 170

Hello R experts, I am trying to analyze this dataset and am stuck on this problem for quite some time now. I am using mt.rawp2adjp. the output that came out was a matrix with two colums since I had asked it to calculate the adjusted p values using one method. so it has the two columns as: rawp BH I combined these using cbind with my actual dataframe. checked using head all was fine. thereafter I

drm_sched_init() has a great many parameters and upcoming new functionality for the scheduler might add even more. Generally, the great number of parameters reduces readability and has already caused one missnaming in: commit 6f1cacf4eba7 ("drm/nouveau: Improve variable name in nouveau_sched_init()"). Introduce a new struct for the scheduler init parameters and port all users.

https://bugs.freedesktop.org/show_bug.cgi?id=103689 Bug ID: 103689 Summary: there is an exploitable page fault that can be reliably triggered from the chromium sandbox can possibly lead to remote attackers causing a denial of service condition or possibly running system code. Product: xorg