Convert genotype matrix into plink format

[pepsimax]

I have a genotype matrix (700 000 rows of SNPs and 2000 columns of samples). It's coded as 0/1/2 or NA. I want to convert this into plink format ped and map files. What's the best way to do this?

Thanks for the help!

[gringer]

With that format of one line per SNP, you're better off creating a TPED (transposed pedigree) file, and then creating PED/MAP (if necessary) from that using PLINK:

http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr

You'll need to recode your genotypes with actual bases depending on the variant, and create dummy parents and/or phenotypes for the individuals in the MAP file.

The biggest problem I have had with TPED format is that it requires location information to be stored for the variants in the TPED file.

Note that PLINK is able to handle TPED files as input, so unless you're using another program for analysis, you can keep the data in that format.