Export tped file to R

Question

[more.u88]

Hi all!

I'm writing this post because I have a problem to export .tped file into R. I used this command in R:

convert.snp.tped (tped="name of tped file", tfam="name of tfam file", out="namedataset.raw")

and I got this error:

"Error in convert.snp.tped : coding 'RD' for SNP not recognised!"

I used this command with files of small dimensions in order to learn the commands in GenABEL and it worked well but when I used the same command for my big files I obtained that error and I'm not understanding. Also, since my file is very big, I checked the first rows of the tped file in order to check the snp identifier and it starts with 'rs'.

Someone have some suggestions to solve this problem? Thank you

[Kevin Blighe]

On which operating system did you produce the tped file, and on which are you trying to execute convert.snp.tped?

[Kevin Blighe]

There is logic to my comment (above). The error has been reported elsewhere without a valid solution, from what I can see. I figured that there could be some encoding issue between different operating systems.

Answer 1

[more.u88]

Hi! thank you for your answer. I read only now your message. Finally, I fixed it. There were some errors in the original file, indeed some SNPs were codified with R or D code instead of A,C,G,T. Therefore, I removed directly these SNPs using PLINK and now I can export the file in R.

[Kevin Blighe]

Great thanks - You can 'Accept' your own answer, in that case.