Question: Is it possible to convert back to .ped from .raw (made with plink)?
0
gravatar for meri.kaustio
19 months ago by
meri.kaustio0 wrote:

Hi,

I got some genotype data as .map and .raw files, so I don't have the original ped-file. Is there some easy way to convert back to .ped format? I found that his question had been asked here before but there wasn't really an answer.

If there is no way to convert back to ped-format, would anyone be able to tell me or stear me towards information on what to do with the -raw file or how to handle it in R? I'd like to be able to find genotypes for specific snps at least, but I'm not familiar with R or this file format and don't really know where to start...

Cheers, Meri

ped plink raw R • 827 views
ADD COMMENTlink written 19 months ago by meri.kaustio0

From what I can see, in PLINK, the raw file is just a phenotype file that has the following format:

FID    IID      pheno1   pheno2    pheno3 ... phenoX

If you only have that plus the MAP file, then you won't have any genotype information and you therefore will not be able to create a PED file.

Can you run the BASH head() command on your raw file?

ADD REPLYlink written 19 months ago by Kevin Blighe41k

See Plink Raw Format To Ped Format and How to convert plink.raw to map and ped files in any software for further information

ADD REPLYlink written 17 months ago by Kevin Blighe41k
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