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Question: PLINK - Obtaining polygenic score
0
gravatar for amalia
4.6 years ago by
amalia • 0
Netherlands
amalia • 0 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 • 5.2k views
ADD COMMENT • link •
modified 4.6 years ago by Nandini • 830 • written 4.6 years ago by amalia • 0
0
gravatar for Nandini
4.6 years ago by
Nandini • 830
London
Nandini • 830 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 COMMENT • link modified 4.6 years ago • written 4.6 years ago by Nandini • 830

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 REPLY • link written 4.6 years ago by amalia • 0
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