similar to: Incomplete Trio in TDT analysis

I am using dgc.genetics to perform TDT analysis on SNP data from a cohort of trios. I now have a file with about 6008 variables. The first few variables related to the pedigree data such as the pedigree ID the person ID etc. Thereafter each variable is a specific locus or marker. The variables are named by a pattern such as "Genotype.nnnnn" with nnnnn corresponding to a number which

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

Dear List, My first R function is a rip-off bagging algorithm from pg. 138 of Everitt and Hothorn's "Handbook of Statistical Analyses using R" (HSAUR). I'm using recursive partitioning to develop a set of useful variables in diagnosing ADHD. I'm running this in ESS in XEmacs 21.4.19, R 2.4.1 on Slackware Linux 11.0 with a 2.6 kernel. This is almost an entire script,

Dear R listers, I have a data file looks like the following: Testing marker: s_1 --------------------------------------------- Allele df(0) -LnLk(0) df(T) -LnLk(T) ChiSq p 3 7995 29320.30 7994 29311.85 16.90 4e-05 (2229/8000 probands) Testing marker: s_2 --------------------------------------------- Allele df(0)

Does anyone know if the sib TDT has been implemented in R 1. Spielman, R.S., and Ewens, W.J. (1998) A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test. Am J Hum Genet 62, 450-458 -- Farrel Buchinsky, MD Pediatric Otolaryngologist Allegheny General Hospital Pittsburgh, PA

Hi, can anyone help me fit betabinomial model to the following dataset where each iD is a cluster in itself , if i use package aod 's betabinom model it gives an estimate of zero to phi(the correlation coeficient ) and if i fix it to the anova type estimate obtained from icc( in package aod) then it says system is exactly singular. And when i try to fit my loglikelihood by

I am about one step away from heaven on earth. I think only one step! I am using dgc.genetics to run a TDT test on thousands of genetic loci. I have learnt (through the help of others on this mailing list) to send the complex output to useful data frames which in turn allow me to look at the big picture and screen the thousands of loci. Resultdt<-lapply(PGWide[,240:290], tdt) the above

Hello, I have been using Xen on a Debian Lenny server for quite some time. I decided to build a new Dom0 using identical hardware, but newest version of Xen from repositories with Debian Squeeze. I attempting to create a new DomU on the new host which is similar to an existing DomU running on the older Lenny host. The DomU is a three NIC firewall. Two of the NICs are virtualized. One NIC is a

Hello, my server has massive problems with my NIC. I got: "Detected Tx Unit Hang". At the moment I use 2.6.31 from Jeremy, does anyone know if it''s fixed in 2.6.32 or newer tree? Regards, Stefan Kuhne _______________________________________________ Xen-devel mailing list Xen-devel@lists.xensource.com http://lists.xensource.com/xen-devel

I have three different types of CentOS 6 Xen 4.4 based hypervisors (by hardware) that are experiencing stability issues which I haven't been able to track down. All three types seem to be having issues with NIC and/or PCIe. In most cases, the issues are unrecoverable and require a hard boot to resolve. All have Intel NICs. Often the systems will remain stable for days or weeks, then

How does one create a vector whose contents is the list of variables in a dataframe pertaining to a particular pattern? This is so simple but I cannot find a straightforward answer. I want to be able to pass the contents of that list to a "for" loop. So let us assume that one has a dataframe whose name is Data. And let us assume one had the height of a group of people measured at

Last Friday, Gregory Chaitin (http://www.umcs.maine.edu/~chaitin/lm.html) mentioned that there can be no proof that a given code is the shortest for a problem, even within a language. Still, the script below, a replacement of the "TDT", one of the most frequently used tests in genetics (http://mustat.rockefeller.edu under "downloads") may get close. It contains a few

hello I'm having 2 problems with rsync... one is consequence of the other 1) I'm running an rsyncd one a server... then I run rync (client) as root on another server even being root, it doesn't read files/dirs with chmod 000 for example and gives error on them 2) when these error happens, it happens "IO error encountered" and it skip the "--delete" (I tried

Hi Mr Tierney, I have noticed an error message from R 1.12.x's CMD check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+) e.g.: http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html ---------------- * checking R code for possible problems ... NOTE Warning: non-unique value when setting 'row.names': ?new? Error in

Dear R mailing list, I have a dataset with genotypes from trios and I would like to infer haplotypes for each mother, father and child. The package that I could find that can do this is tdthap. But when the mother is homozygous (e.g., 2/2) the haplotype is called as not possible to infer (0); I would prefer for it to call the genotype (2). From what I understand it is doing what I would like

Greetings all The help file for GAMM in mgcv indicates that the log likelihood for a GAMM reported using summary(my.gamm$lme) (as an example) is not correct. However, in a past R-help post (included below), there is some indication that the likelihood ratio test in anova.lme(mygamm$lme, mygamm1$lme) is valid. How can I tell if anova.lme results are meaningful (are AIC, BIC, and logLik

On Wed, Sep 06, 2023 at 09:55:49AM +0200, Niklas Schnelle wrote: > On Mon, 2023-09-04 at 17:33 +0100, Robin Murphy wrote: > > On 2023-09-04 16:34, Jean-Philippe Brucker wrote: > > > On Fri, Aug 25, 2023 at 05:21:26PM +0200, Niklas Schnelle wrote: > > > > Add ops->flush_iotlb_all operation to enable virtio-iommu for the > > > > dma-iommu deferred flush

On Wed, Sep 06, 2023 at 09:55:49AM +0200, Niklas Schnelle wrote: > On Mon, 2023-09-04 at 17:33 +0100, Robin Murphy wrote: > > On 2023-09-04 16:34, Jean-Philippe Brucker wrote: > > > On Fri, Aug 25, 2023 at 05:21:26PM +0200, Niklas Schnelle wrote: > > > > Add ops->flush_iotlb_all operation to enable virtio-iommu for the > > > > dma-iommu deferred flush

I tried to reproduce a result from a former colleague which he got with S-plus bootstrap method. I don't have S-plus at hand. In R, there are 2 packages related to bootstrap method, bootstrap and boot. The former has a function called 'bootstrap' but this does not seem to conform either to the function used in S-plus nor to that described in MASS, 3d ed., p.144. The latter seems to be

Dear Friends. I am just starting to use R. And in this occasion I want to construct a high-dimensional contingency table, because I want to crate a mosaic plot with the vcd package. My table is in this format: año ac.rep cat.gru conteos 1 2005 R parejas 253 2 2005 N parejas 23 3 2006 R parejas 347 4 2006 N parejas 39 5 2007 R