PED & MAP file extension

Question

[Rakan]

Hi everyone,

I'm trying to upload the PED & MAP file (tab-delimited file) into gplink to run the association test but it doesn't seem that it recognize it? I feel I'm missing some steps in between?! I followed the instruction on plink site on how to create PED & MAP file. How can I convert the txt format into Ped, MAP extension file so I can work on them?

Any thoughts are appreciated.

[alesssia]

it doesn't seem that it recognize it

What error do you receive? PED and MAP file are text files..

[Rakan]

I'm receiving this error plink cannot execute this command locally

[alesssia]

And what is this command? Perhaps giving us some more context (how the file are formed, which command are you running, the precise error you receive...) will help us in replying :)

[kumar.vinod81]

You can do one thing easily if you've a small data set, just format your data set into hapmap format and import in TASSEL and export for plink input.

Answer 1

[Fabio Marroni]

Hi!

A good thing to do when using new software is to use the example data that is usually provided with it.

If you give a look at this page you will see there is a data set: http://pngu.mgh.harvard.edu/~purcell/plink/tutorial.shtml

If you have the same error message with the example data, then the problem is not (as I suspect) a problem of file format.