Question: PLINK - Obtaining polygenic score
0
gravatar for amalia
4.0 years ago by
amalia0
Netherlands
amalia0 wrote:

Hi,

I am trying to obtain in PLINK the polygenic scores of a sample of individuals. I simulated a very simple example to see whether I could make it work, but it seems that it is not. 

I have simulated data for 3000 individuals and 2 SNPs. I created a file .raw that has three columns: SNPid, Reference allele, and score. In the score column I put the log of odds ratio for significantly associated SNPs. In the reference allele column I just ranfomly set everything to "A", but I do not know whether this is correct, and possibly this is why I am getting an error afterwards. I ran the --score command in plink and I obtain a file where the "score" column is all "0".

Can anyone help?

What do I have to put for "reference allele" if my data is simulated?

Thanks

 

 

 

snp • 4.5k views
ADD COMMENTlink modified 4.0 years ago by Nandini780 • written 4.0 years ago by amalia0
0
gravatar for Nandini
4.0 years ago by
Nandini780
London
Nandini780 wrote:

So, Your score file should have lines looking like

SNP1 allele_effected Score

The second column is not a 'reference allele', it is more of the affected allele for that SNP that contributes to the score.

There are many tutorials out there, for example this one

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Nandini780

Thank you! 

I have a more basic question then. I simulated data for 3000 individuals and 2 SNPs. For the 2 SNPs I simulated two columns for each, one indicating the allele on the chromosome inherited from the mother and another one from the father. I have filled up these two columns with a lot of 1 and 2's. However, In my .raw file I need to state which is the allele_effected in terms of "G-C-T-A". How do I know this from my simulation?

What do these 1 and 2's that I have simulated mean??

Can I put in my .raw file a 1 or a 2 as allele_effected?

ADD REPLYlink written 4.0 years ago by amalia0
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