similar to: A question about GRAMMAR calculations in the FAM_MDR algorithm

I have a few questions about GenABEL, gwaa data. 1) is there a universal way that most GenABEL people use to add more individuals into a 'gwaa' data? For example, I have a 'gwaa' data, but I need to add some dummy parents, for 'gwaa at phdata', it's easy to add these rows, but for 'gwaa at gtdata', I think I need to create SNP data as '0 0 0 0 0.....'

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,

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

Hi, I'm using kinship2 to calculate heritabilty, but I would like calculate in GenABEL too. I trying the code: > require(kinship2) > require(GenABEL) > pedig = with(Dados, pedigree(id=IID, dadid=PAT, momid=MAT, sex=SEX, famid=FID, missid=0)) > kmat = kinship(pedig) > (mod1 = polygenic(altura ~ SEX + idade, data=Dados, kin=kmat)) Erro em intI(i, n = d[1],

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

I just upgrdaded to FreeBSD 5.2 CURRENT and installed samba 3.0.3pre2. I have copied /etc/printcap and samba config from the previous installtion (FreeBSD 4.8 and samba 2.x) Now, i cannot print anything from windows xp (i only have windows xps, so i cannot tell if it works from other windows but i guess it does not). When i printed the data is sent to the printer and no error shows up on

FYI. There is a Thai vignette - and it went a lot further doing some Thai text processing in R, than the earlier Chinese/Tibetan/LiangshanYi/Arabic vignette, which was in reality just Chinese + Cairo graphics. Managed to cross-compile an R package for Mac OS X from Linux; and it seems to be working. See screenshots below. I'd be interested to know if there are less obvious bugs; however

I''ve just pushed vdiskadm import/export/convert to the 3.3 vdisk and vbox repos. You can now import a disk image from a block device or file to a vdisk, convert (in place) to a different type of vdisk and export from a vdisk to a block device or file. I''ve also pushed the full vhd support (sparse and fixed) and the ability to import a vmdk 1.1 optimized stream file. An

I've looked through all of the posts about this issue (and there are plenty!) but I am still unable to solve the error. ERROR: cannot allocate vector of size 455 Mb I am using R 2.6.2 - x86_64 on a Linux x86_64 Redhat cluster system. When I log in, based on the specs I provide [qsub -I -X -l arch=x86_64] I am randomly assigned to a x86_64 node. I am using package GenABEL. My data (~ 650,000

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

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") :

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

I'm trying to: Resample with replacement pairs of distinct rows from a 120 x 65,000 matrix H of 0's and 1's. For each resampled pair sum the resulting 2 x 65,000 matrix by column: 0 1 0 1 ... + 0 0 1 1 ... _______ = 0 1 1 2 ... For each column accumulate the number of 0's, 1's and 2's over the resamples to obtain a 3 x 65,000 matrix G. For those

Hi all! I am desperately trying to figure out the solution to this error, but nothing as of yet is working. As noted in an earlier post I am using GenABEL. In an attempt to read in the phenotype file, in the format .dat, R keeps giving me the error "more columns than column names" I have tried to read in the data without the headers; I have also tried to trim the data to remove any

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, 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

This appears to be a pthreads problem, not scsi. Anyone care to look at it? ---------- Forwarded message ---------- Date: Wed, 20 Aug 2003 11:24:42 -0400 From: Dan Langille <dan@langille.org> To: freebsd-scsi@freebsd.org Cc: Kern Sibbald <kern@sibbald.com> Subject: (Fwd) Lost data on FreeBSD tape I've been working with Kern Sibbald, author of Bacula (http://www.bacula.org/) to

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.

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

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