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.....' 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 'gwaa at gtdata' directly,
without
converting data of other format to 'gwaa at gtdata' first?
thank you very much!
karena
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