similar to: Kinship2 and GenABEL

Dear R developers: I am a PHD candidate student in the school of public health of Peking University and my major is genetic epidemiology. I am learning the FAM-MDR algorithm, which is used to detect the gene-gene and gene-environment interactions in the data of pedigree. The codes were written by Tom Cattaert of the University of Liege. The algorithms and the sample datasets are available at

I am making the question clear. Please help. > Dear R experts > > I was using kinship package to fit mixed model with kinship matrix. > The package looks like lme4, but I could find a way to extract p-value > out of it. I need to extract is as I need to analyse large number of > variables (> 10000). > > Please help me: > > require(kinship) > > #Generating

Dear R experts I was using kinship package to fit mixed model with kinship matrix. The package looks like lme4, but I could find a way to extract p-value out of it. I need to extract is as I need to analyse large number of variables (> 10000). Please help me: require(kinship) Generating random example data id <- 1:100 dadid <- c(rep(0, 5), rep(1, 5), rep(3, 5), rep(5, 5), rep(7,

Hi, I am using a function 'polygenic' in the package called 'GenABEL'. -------------------------------------------------------------------------------- > h2.gs <- polygenic(b.dbp~age+age2+age3+sex+b.bmi, kin=gs.gkin, data=gs) ------------------------------------------------------------------------------- ## and I got the following error message: Error in svd(X): infinite or

Dear Sir/Madam, Since a few day now I try to use the command "polygenic" from the GenAbel package. However, I keep bumping up against an error message: "Error in polygenic(Testo, kin = kinship, data = data1) : dimension of outcome and kinship.matrix do not match". My data exists of 1240 individuals with 74 markers. It mainly consists of small families (2 or more brothers,

Dear useRs: Announcing the release of kinship2, version 1.2.1, to CRAN. kinship2 is a branch from the original kinship package with some key updates for the pedigree and kinship functions, with some additional functions that work with the pedigree object. Highlights: * pedigree and pedigreeList objects implemented with S3 methods print and "[," * pedigree plotting routine

Dear useRs: Announcing the release of kinship2, version 1.2.1, to CRAN. kinship2 is a branch from the original kinship package with some key updates for the pedigree and kinship functions, with some additional functions that work with the pedigree object. Highlights: * pedigree and pedigreeList objects implemented with S3 methods print and "[," * pedigree plotting routine

Does anyone use the R library GenABEL? I am using it to calculate SNP interactions. I have a list of 100 SNPs, I need to look at the interaction between each of two SNPs among the list. my question is how to perform this in GenABEL. I want to use the "lm" function, but don't know how to use the SNP information. for example: result <- (lm(y~SNP1+SNP2+SNP1*SNP2)) the problem here

Dear all, since yesterday, I have been experiencing problems with the package GenABEL. When I try to load the package (library(GenABEL)) I get the following error message: Loading required package: MASS Error : .onLoad failed in loadNamespace() for 'GenABEL', details: call: stringSplit[[1]] error: subscript out of bounds Error: package/namespace load failed for ?GenABEL? The funny

Hi, I've been trying to use the impute2mach function in the GenABEL library. I unfortunately cannot make a working example as when I scale down the files I no longer get an error message. The error message that I get on the full file is: Error in checkSlotAssignment(object, name, value) : assignment of an object of class "NULL" is not valid for slot "data" in an

Hi all! I am using GenABEL on R for GWAS analysis. I am having a couple of issues: First, I am having a problem reading files (.map, & .ped, size 900Mb, using windows 32-bit) onto R in the "convert.snp.ped" statement. I am thinking this problem is likely due to the large size of the files & my version of R is not able to handle them, since I can read in smaller files.

I've been looking at the kinship package which looks as though it might be appropriate for my purposes. What I can't find is any reference to the data that is used in the example code. A dataframe called d10 with column names, upn, dadid, momid, sex and affect is required. One can get an idea of what sort of values should be in most columns from the description in the pedigree function,

Hi Im using the kinship package to draw a pedigree. On my data set this works fine but when i add indivudals to the pedigree i keep getting an error i hope someone can help me! This is the code im using: Data<-read.table("Tree.txt", header=T, sep=",") attach(Data) ped<-pedigree(id, dadid, momid, sex, aff) par(xpd=T) plot.pedigree(ped) This is my data looks like

Hi all! I am trying to install package - GenABEL in a Linux (RedHat) environment using R 2.6.2. The CRAN Mirror starts up, I select the site, but I end up with the following error: ****************************************************************** Warning: unable to access index for repository http://cran.stat.ucla.edu/src/contrib Warning messages: 1: In open.connection(con, "r") :

Hi,I use the 'lmekin' model of the 'kinship' package of R in order to estimate heritability. I want to estimate the confidence interval of the variance coefficient and so I should use a bootstrap simulation. The pedigree file has 1386 subjects so I create a kinship matrix [1386*1386].This is the code of R I use: kfit2 <- lmekin(IT~1+AGE +(1|ID), dati1,

I have library in development with a function that works when called from the top level, but fails under R CMD check. The paricular line of failure is rsum <- rowSums(kmat>0) where kmat is a dsCMatrix object. I'm currently stumped and looking for some ideas. I've created a stripped down library "ktest" that has only 3 functions: pedigree.R to create a pedigree or

Hi, I had originally posted regarding an error when trying to install package - GenABEL - it has now become clear that R is not able to connect to the net. Below are a couple of things I've tried with the resulting errors I am running R 2.6.2 on Linux e15 X86 How can I fix this? Thank you! 1) download.file("http://www.nytimes.com", destfile<-tempfile()) Error: trying URL

Thanks for the feedback Dirk. I sent my follow-up before I saw it. Looking at the source code, it appears that there is no options() call to turn this on. Nor does "R --help" reveal a command line option. How then does a user turn this on outside of the R CMD check envirionment, so as to chase things like this down? The fact that 1. renaming my function makes the error go away, 2.

Hello, All, GWAF 1.2 R.Version() is below. system(lme.batch.imputed( phenfile = 'phenfile.csv', genfile = 'CARe_imputed_release.0.fhsR.gz', pedfile='pedfile.csv', phen='phen1', covar=c('covar1','covar2'), kinmat='imputed_fhs.kinship.RData', outfile='imputed.FHS.IBC.GWAF.LME.output.0.txt' )) Gives the error messages: Error in

Someone just sent me a data set that causes the lmekin function, part of the kinship package, to fail. In chasing it down I get an error I have never seen before. fit <- lmekin(icam1 ~ factor(center) + age + factor(sex), random= ~1|iid, data=chaidata, varlist=kmat) Error in Y - fitted : non-numeric argument to binary operator Add the recover option, and the offending lines are