search for: hapassoc

Version 1.0 of hapassoc now available from CRAN hapassoc is an R package for likelihood inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm. Recent changes include the addition of anova and logLik methods for the class hapassoc, to allow users to perform likelihood ratio tes...

Version 1.0 of hapassoc now available from CRAN hapassoc is an R package for likelihood inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm. Recent changes include the addition of anova and logLik methods for the class hapassoc, to allow users to perform likelihood ratio tes...

Dear Sir/Madam, I am running a R program for my SNP data. There are some errors when I run glm model in Hapassoc software, sometimes it is over the memory and sometimes the matrix is singular. I want to ingore these errors and excute the next statement. Otherwise, I have a big big trouble. Do you have some idea about this problem of ingore errors. Wish to get your help assp. thanks. -- Wei Guo Department...

...;) #rejected because I subjectively think we don't need them failPackages2 <- c("aaMI","AlgDesign","bim","caMassClass","CGIwithR","CDNmoney","clac","clim.pact","compositions","cyclones","hapassoc","haplo.score","haplo.stats","hapsim","httpRequest", "labdsv","kza","LMGene","Malmig","magic","negenes","oz","papply","spe","wavethresh","waveslim&qu...

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

Hello to everyone! I have built CRAN task view for genetics. For now I have not submit it to CRAN yet and it can be accessible from: http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.html http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.ctv I have not submitted it to CRAN, since I would like first some opinion about it. Genetics is really so broad field that I belive one person

...ot;,"graphics","grasper","GRASS","gRbase","grDevices","gregmisc","grid","gridBase","grnnR","grouped","GroupSeq","gss","gstat","gsubfn","gtools","hapassoc","haplo.ccs","haplo.stats","hapsim","hddplot","hdf5","hdrcde","hett","HI","hier.part","hierfstat","HighProbability","Hmisc","hmm.discnp","homals","ho...

CRAN (and crantastic) updates this week New packages ------------ * EffectStars (1.0) Maintainer: Unknown Author(s): Gunther Schauberger License: GPL-2 http://crantastic.org/packages/EffectStars The package provides functions to visualize regression models with categorical response. The effects of the covariates are plotted with star plots in order to allow for an optical

...pCns@mail.gmail.com> Content-Type: text/plain; charset=windows-1252 You could do a weighted cox ph model, with possible haplotype configurations for each subject weighted by their posterior probabilities given genotype data. Are your markers SNPs? If so you can use a utility function from the hapassoc package to get started. For example, if your data is in a dataframe dat, with nsnp SNPs in the last nsnps columns, you could create an augmented data frame (augmented by pseudo-individuals for each subject with ambiguous phase) with library(hapassoc) ph<-pre.hapassoc(dat,nsnps) augdat<-cbind...

...1), GExMap (1.1), ggplot2 (0.8.8), ghyp (1.5.3), glmnet (1.4), gmm (1.3-2), gplots (2.8.0), gputools (0.21), gRain (0.8.5), grImport (0.6-1), gss (1.1-5), gsubfn (0.5-3), gtools (2.6.2), gWidgets (0.0-41), gWidgetsRGtk2 (0.0-67), gWidgetsrJava (0.0-19), gWidgetstcltk (0.0-38), gWidgetsWWW (0.0-19), hapassoc (1.2-4), hash (2.0.1), hergm (1.2-5), hglm (1.1.1), highlight (0.2-1), Hmisc (3.8-2), hopach (2.9.1), ibr (1.2.2), identity (0.2-1), ifultools (1.0-7), imprProbEst (1.0.1), impute (1.22.0), imputeMDR (1.1), inline (0.3.5), inlinedocs (1.1), intamapInteractive (1.0-9), intervals (0.13.2), introgress...