search for: hwe

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...

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 2 alleles scen...

...ot; "G/G" "G/G" "G/G" "G/G" "G/G" "G/G" "G/G" "G/G" "G/G" [73] "G/G" "G/G" "G/A" "G/G" "G/G" "G/G" "G/G" "G/G" Alleles: G A > HWE.exact(g1) Exact Test for Hardy-Weinberg Equilibrium data: g1 N11 = 71, N12 = 9, N22 = 0, N1 = 151, N2 = 9, p-value = 1 > control.data <- c("G/G","G/G","G/G","G/G","G/G","G/G","G/G","G/G","G/G&quot...

...o-common -g -O2 -c gif.c -o gif.o gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c hap.c -o hap.o gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c hwe.hardy.c -o hwe.hardy.o gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c kin.morgan.c -o kin.morgan.o gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2...

...omosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, computing disequlibrium, testing Hardy-Weinberg equilibrium, ... License: GPL Built: R 1.6.0; sparc-sun-solaris2.8; Tue Nov 12 15:43:20 EST 2002 Index: HWE.test Estimate Disequlibrium and Test for Hardy-Weinberg Equilibrium ci.balance Experimental Function to Correct Confidence Intervals At or Near Boundaries of the Parameter Space by 'Sliding'...

...omosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, computing disequlibrium, testing Hardy-Weinberg equilibrium, ... License: GPL Built: R 1.6.0; sparc-sun-solaris2.8; Tue Nov 12 15:43:20 EST 2002 Index: HWE.test Estimate Disequlibrium and Test for Hardy-Weinberg Equilibrium ci.balance Experimental Function to Correct Confidence Intervals At or Near Boundaries of the Parameter Space by 'Sliding'...

...r this warning. The package i have made, builds, installs and works well, except for this warning when I check it: When I run: R CMD check mypack_1.0.tar.gz ... ... .. .. * checking R code for possible problems ... NOTE Found possibly global 'T' or 'F' in the following functions: HWE procRef readMartFile readPhase2File .. ... .. I have several other functions in the package, but the warning is for this subset. I am trying to find a common thing within this subset, and cant figure out one to go after it. Thanks a lot for the help. Regards, Sahil Seth

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 return of the function does not have classical components for htest class so I was afcourse not successfull in using it. However, I managed to copy and modify some part of prin...

...olution from 4K (3840x2160) to 2K (1920x1080) (and probably any other resolution) causes the screen to go black. with the older Nouveau driver included in Kubuntu 16.04.2 (Ubuntu 16.04.2) changing the display resolution from 4K to 2K works fine. Kubuntu 16.04.2 uses the xserver-xorg-video-nouveau-hwe-16.04 package at version 1:1.0.12-2~16.04.1. Kubuntu 16.04.3 uses the xserver-xorg-video-nouveau-hwe-16.04 package at version 1:1.0.14-0ubuntu1 apparently the change from 1.0.12 --> 1.0.14 broke the ability to change the screen resolution. but on the plus side, the Nouveau driver in 16.04.3 (...

...ort the single patch you need: https://github.com/libguestfs/supermin/commit/158854e3ba4be7f6b8d81f662ddad98358ede1de This should apply fine to the older version of supermin. By the way, there has now been a bug opened in launchpad about this: https://bugs.launchpad.net/ubuntu/+source/linux-hwe/+bug/1743300 Rich. -- Richard Jones, Virtualization Group, Red Hat http://people.redhat.com/~rjones Read my programming and virtualization blog: http://rwmj.wordpress.com virt-builder quickly builds VMs from scratch http://libguestfs.org/virt-builder.1.html

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

...40 50 100 30 60 120 So the row totals are fixed. Is this the correct code3? Likelihood.ratio = dmulitnom(100, c(0.1, 0.2, 0.7))*dmultinom(100, c(0.2, 0.4, 0.5)) divided by dmulitnom(100, c(0.33, 0.33, 0.34))*dmultinom(100, c(0.33, 0.33, 0.34)) What about if the null came from the HWE proportions how will this work for the case control SNP situation? -- Thanks, Jim. [[alternative HTML version deleted]]

...ing... # Contacting target "qhus029"... # # Target: qhus029:/ # # # Bundle(s): # A5230A B.10.20.01 HP-PCI 100Mb LAN/9000 B3920CA B.10.20 HP-UX Media Kit (Reference Only. See Description) B7682AA B.10.20.HWE.3 Hardware Extensions 3.0 for HP-UX 10.20 HPUXEngCR800 B.10.20 English HP-UX CDE Runtime Environment J3620BA B.10.20.07 100BT/9000 GSC for K and T Series J3630BA B.10.20.61 Fibre Channel Mass Storage Driver J4188-1...

...tes. Specifically, it affects summary(data.frame) with some columns that contains NA's. Here is an edited example snipplet (you should view this with fixed-width font terminal): ================= \begin{Sinput} > summary(some.data.frame) \end{Sinput} \begin{Soutput} P.BB z.HWE Min. :0.00000 Min. :-3.83163 1st Qu.:0.07071 1st Qu.:-0.56856 Median :0.26263 Median : 0.18426 Mean :0.33754 Mean : 0.06581 3rd Qu.:0.56566 3rd Qu.: 0.73845 Max. :0.98990 Max. : 3.73120 NA's :2 \end{Soutput} ======...

...successfully unpacked and MD5 sums checked Delete downloaded files (y/N)? y updating HTML package descriptions > library("gap") Error in library("gap") : There is no package called 'gap' > library("gap", lib.loc="C:/Programs/R/library") > ?hwe.hardy I also reported yesterday that this is not 100% reproducible. I tried to install today bundle 'gregmisc' and the installation failed only partly, due to failure of moving temporary installation directory for 'gplots', while others packages passed OK. Strange. Look below: &g...

...browse[2658]] Nov 10 11:24:37 nitro kernel: [ 196.887274] nouveau 0000:01:00.0: fifo: gr engine fault on channel 8, recovering... Nov 10 11:24:57 nitro kernel: [ 216.884429] ------------[ cut here ]------------ Nov 10 11:24:57 nitro kernel: [ 216.884467] WARNING: CPU: 2 PID: 1032 at /build/linux-hwe-lyR8gz/linux-hwe-4.10.0/drivers/gpu/drm/nouveau/nouveau_bo.c:1212 nouveau_bo_move_ntfy+0xa3/0xb0 [nouveau] Nov 10 11:24:57 nitro kernel: [ 216.884467] Modules linked in: nls_utf8 udf crc_itu_t nls_iso8859_1 hid_multitouch intel_rapl x86_pkg_temp_thermal intel_powerclamp joydev coretemp kvm uvcvide...

...he driver didn't work at all for the NV43 gpu few years ago but now it is working but not stable yet. I am on Ubuntu 18.04.3 LTS, tested on kernels 4.15/4.18/5.0, xserver-xorg-video-nouveau 1:1.0.15-2, libdrm-nouveau2 2.4.97-1ubuntu1~18.04.1 Have also tested it with xserver-xorg-video-nouveau-hwe-18.04 1:1.0.16-1~18.04.1 dmesg is full of these lines: [ 199.658774] nouveau 0000:04:00.0: systemd-logind[1352]: validate: -22 [ 199.658902] nouveau 0000:04:00.0: systemd-logind[1352]: fail set_domain [ 199.658905] nouveau 0000:04:00.0: systemd-logind[1352]: validating bo list [ 199.658907] nou...

https://bugs.freedesktop.org/show_bug.cgi?id=110500 Bug ID: 110500 Summary: X-Server crashes - GL error: GL_OUT_OF_MEMORY in glTexSubImage Product: Mesa Version: unspecified Hardware: x86-64 (AMD64) OS: Linux (All) Status: NEW Severity: major Priority: medium

uname -a Linux drh-MS-7888 4.13.0-26-generic #29~16.04.2-Ubuntu SMP Tue Jan 9 22:00:44 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux dpkg -l libguest* Desired=Unknown/Install/Remove/Purge/Hold | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad) ||/ Name Version Architecture