similar to: help needed for HWE.exact in library "genetics"

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

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

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, 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

I evaluated the Bayes factor in the k=2 allele case with a "triangular" prior under the null as in the example in the help file: HWETriangBF2(nvec=c(88,10,2)) [1] 0.4580336 When I swap the n11 entry and n22 entry of nvec, I received totally different Bayes factor: > > HWETriangBF2(nvec=c(2,10,88)) [1] 5.710153 > In my understanding, defining the genotype frequency as

Has something changed in R that requires an update in the genetics package by Gregory Warnes? I am using R version 2.5.0 This used to work > summary(founders[,59]) to prove that it is a genotype class > class(founders[,59]) [1] "genotype" "factor" Now when I issue the command: > summary(founders[,59]) I get: Error in attr(retval, "which") <- which :

Hello, I am having really hard time finding a good article about simulating genotypes of cases and controls at a disease locus using R. if you guys can point me or guide me where i can find more information, it will be helpful. thanks, Claire -- View this message in context: http://www.nabble.com/genotypes-simulation-tp17065607p17065607.html Sent from the R help mailing list archive at

I'm wondering how odds ratio is computed. I thought that it is (n11/n12)/(n21/n22), but it is not what fisher.test() computes. Could somebody let me know? > n11=3 > n12=1 > n21=1 > n22=3 > > n1_=n11+n12 > n2_=n21+n22 > > n_1=n11+n21 > n_2=n12+n22 > > x=rbind(c(n11,n12),c(n21,n22)) > > threshold=dhyper(n11,n1_,n2_,n_1) >

Hi, this is my first time using R. I want to simulate the following process: "in a population of size N, there are i individuals bearing genotype A, the number of those bearing A is j in the next generation, which following a binominal distribution (choose j from 2*N, the p is i/2*N), to plot the probability of the next generations, my script is as follows. It cannot run successfully,

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

Dear Sir, We need to use genetics packages at our end. We have installed R packages. When i try to choose genetics package and install, it is giving an error. Please see the attachment for the error. How can i resolve it and make it work? Thanking you A Padmavathi Devi Technical Officer Centre for Cellular and Molecular Biology Ph.No:27192776 "The person addressed in the email is the sole

Dear all, we seek a talented and motivated post-doc to develop computational methods for inferring the molecular basis of genetic diseases by integration of personal omics data. Research topics include: identifying causal mutations of rare disease patients by meta-analysis; inferring disease-causing molecular pathways from genotype, phenotypes, and omics profile of patient-derived cell lines

Hi everybody, I've been looking for a function that combines all variables from a dataset because I need to do multivariate regression. If we have linear regression with an expression like f(x) = a0 + sum(ai*xi) what I want to do is something like f(x) = a0 + sum(ai*xi) + sum(sum(bij * xi * xj)) + sum(sum(sum(cijk*xi*xj*xk))) + ... So I need a function that combines all the values from

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

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]]

I have been trying to determine the size of the R user base, and was asked to share my findings with this mailing list. Although I still don't have any definite estimate of this number, I do have some interesting and indicative information: 1. It appears that there are about 100,000 S-PLUS users. Rationale: According to Insightful's 2002 Annual Report, over 100,000 people use

Hello, I have a data with following format:      Predictors          n11     n12     n21     n22     Odds.Ratio    log.ratio    se.log.odds. 1 ProcOR respirato     2 ProcVaric vein      3 DiagCardiac anom   4 DiagAllergy        5  DiagOth skin dx    6    DiagGastritis          I want to plot odds ratio by command: forestplot in rmeta library, but I get the following error constantly.  Error in

I'm new to R (previously used SAS primarily) and I have a genetics data frame consisting of genotypes for each of 300+ subjects (ID1, ID2, ID3, ...) at 3000+ genetic locations (SNP1, SNP2, SNP3...). A small subset of the data is shown below: SNP_ID SNP1 SNP2 SNP3 SNP4 Maj_Allele C G C A Min_Allele T A T G ID1 CC GG CT AA ID2 CC GG CC AA ID3 CC GG nc AA

Dear mailing list, I'm still quite a newbie in the statistical analysis of genotype/allele data, resp. more generally in the analysis of categorical variables. Moreover, I'm currently totally confused by the many R packages available to do such analysis. Here is my case: I've got a list of genes, and a number of case-control population pairs, and for each population and gene, the