search for: pedfile

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 coxme.varcheck(ncluster, varlist, n, gvars, groups, sparse, rescale,...

..., 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.....' for all the dummy parents first. I am using the function 'convert.snp.ped', so I need a 'pedfile' of this format: #ped id fa mo sex trait snp1.allele1 snp1.allele2 snp2.allele1 snp2.allele2 ...# 1 1 0 0 1 2 0 0 0 0 ... 1 2 0 0 1 0 0 0 0 0 ... 1 3 0 0 2 1 0 0 0 0 ... . . 100 101 0 0 2 1 0 0 0 0 ... If we use the 1M microarray, usually, after QC, there will be ~800 thousands SNPs, so this...

...rt of the University of Liege. The algorithms and the sample datasets are available at http://www.statgen.ulg.ac.be/index.php?option=com_content&view=article&id=90&Itemid=85. The R I used is R-2.15.1 in the Windows XP system. The command lines I have run are as follows: # data files pedfile="pedigree1.ped" phenofil="pheno1.dat" mapfile="simulation.map" # solver settings npermute = 1000 # fixed number of permutations, 1000 is recommended alpha = 0.05 # type-I error Pval = 0.1 # significance...

.... (Chinese/Tibetan/Arabic/Liangshan Yi was covered in a different vignette previously). More on this and emacs's multilingual extension further down. "snpMatrix Tutorial 2007" was the first ever tutorial written in spring 2007 [1]; it was pre-vignette and therefore had all the hapmap/pedfile output recorded verbatim; newly revived to work as a testsuite for input/output of hapmap/ped files (and flaged and fixed a few bugs introduced in the last few years). The bug fixes will appear in the upcoming snpMatrix 1.19.0.12, which hopefully will include some continual work to add read.tped()...