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 'g...@phdata', it's easy to add these rows, but for 'g...@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 file is really huge. I created this matrix in R, and then try to export this by using 'write.table(pedfile, file='pedfile', col.names=F, row.names=F, quote=F), but seems like it's taking for ever, because the size of this matrix is too large. Anyone can tell me, how to create a 'gwaa' data efficiently? 2) Is there any way to add genotypic data to 'g...@gtdata' directly, without converting data of other format to 'g...@gtdata' first? thank you very much! karena -- View this message in context: http://r.789695.n4.nabble.com/how-to-handle-gwaa-gtdata-tp3026206p3026206.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
