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Hi, ? I am very new to R. So, pardon my dumb question. I was trying to write my own function to run a different model (perform an ordered logistic regression) using the example in website http://pngu.mgh.harvard.edu/~purcell/plink/rfunc.shtml But R returns a error `R Error in eval(expr, envir, enclos) : object 's' not found' when I run it. What am I doing wrong here? Here's what I got from the debug file. # Input data n <- 10 PHENO <- c( 1, 3, 2, 3, 1, 1, 1, 2, 1, 2 )...

Hi All, does anyone know how to import binary .bed files generated by Plink (http://pngu.mgh.harvard.edu/~purcell/plink/ ) into R? the Plink FAQ explains how to conver other types of files, not the .bed. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941...

I a using plink on a large SNP dataset with a .map and .ped file. I want to get some sort of file say a list of all the SNPs that plink is saying that I have. ANyideas on how to do this? -- Thanks, Jim. [[alternative HTML version deleted]]

...FYI -- This is for storing minor-allele counts for genetic studies. There are 0, 1 or 2 minor alleles and 3 would represent missing.) It is theoretically possible to store such data with four integers per byte. This is what PLINK (GPL license) does in its binary (.bed) pedigree format: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped That might be too much to hope for. ;-) I think that the R system uses double-precision floating point numbers by default. When I impute minor-allele counts, I get posterior expected values ranging from 0 to 2 (called dosages). The imputation isn...

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

...---------------------------------------@ | PLINK! | v0.99p | 17/Dec/2006 | |----------------------------------------------------------| | (C) 2006 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| | http://pngu.mgh.harvard.edu/purcell/plink/ | @----------------------------------------------------------@ ======================================== - XeTeX definitely does not like having any \usepackage[whatever]{inputenc} (it assumes inputs are always utf-8) While both of these can be worked aroun...

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