similar to: sib TDT transmission/disequilibrium test

I am involved in a study where, as in most of life, men demonstrate themselves to be recalcitrant. So while we have many probands and most of their mothers we only have about 50% of the trios being complete. I have been running tdt and trio.types. It appears as if it is ignoring the duos. Sometimes a duo can be informative. For instance Father ..missing Mother 1/2 Proband 1/1 This duo shows that

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

Dear all, I'm using the package "Genetics", and I'm interested in the computation of D' statistics for Linkage Disequilibrium, for which the LD() command has been realised. Unfortunately I don't find any reference on "how" the D' is computed by the LD() function. In the package documentation it is generally referred as "MLE" estimation, but

Dear R helpers, I am trying to test for linkage disequilibrium (LD) in R between all pairs of loci. Importantly, my loci are microsatellites and have up to 30 alleles per locus. Do you know of any R packages that can either (1) calculate measures of LD directly or (2) test for the presence of LD within a statistical framework? Every package I have run across seems to be only able to handle

Dear All, Does anybody have experience with R package pbatR (http://cran.r-project.org/web/packages/pbatR/index.html)? I am trying to use it to analyze the family-based case-control data, but the package totally doesn?t work on my computer. I contacted the authors of the package, but I haven?t heard anything from them. Following the package manual, I tried the simple example as below:

Hi , is it possible to calculate ld-measures D, D', r and perhaps corresponding p-values with r IF THE PHASE IS KNOWN? The genetics - package provides the LD function only for ambigious phase. Thank you very much Bettina Kulle

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

Hello all, I am not sure whether it actually is a bug, but it is not the behaviour I would expect. Please consider this: >Sibships [1] Patient_2400 Patient_2400 Patient_345 Patient_345 Patient_8901 [6] Patient_8901 Patient_4008 Patient_4008 Patient_7991 Patient_7991 [11] Patient_8353 Patient_8353 Patient_1212 Patient_1212 Patient_2168 [16] Patient_2168 Patient_2760 Patient_2760

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

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

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

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 ============================================================================= FreeBSD-SA-04:04.tcp Security Advisory The FreeBSD Project Topic: many out-of-sequence TCP packets denial-of-service Category: core Module: kernel

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 am trying to produce a heatmap of pairwise correlations, but since the matrix is > symmetric, I only need either the upper or the lower triangle. I have scoured the > web and R documentation, but I have not been able to find a way to produce such a > figure. Is there a simple way to produce a heat map with only the part above or > below the diagonal? You might want to check