Polygenic risk score

[Moksedul Momin]

Dear Concern,

Hope you doing well.

I was trying to estimate PRS using the following commands.

./plink2 --bfile toy --linear --pheno toy.dat --allow-no-sex --out toy
./plink1.9 --bfile toy --score toy.assoc.linear --out toy

getting following error

Logging to toy.log.
Options in effect:
  --bfile toy
  --out toy
  --score toy.assoc.linear

3789 MB RAM detected; reserving 1894 MB for main workspace.
2877 variants loaded from .bim file.
1000 people (0 males, 0 females, 1000 ambiguous) loaded from .fam.
Ambiguous sex IDs written to toy.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 1000 founders and 0 nonfounders present.
Calculating allele frequencies... done.
2877 variants and 1000 people pass filters and QC.
Note: No phenotypes present.
Error: No valid entries in --score file.

I will appreciate to solve the problem.

Thanks in advance.

Kindest regards

Momin

-- 

Md. Moksedul Momin

Ph.D. Candidate

University of South Australia

Contact no: +61480242571 

[DAVID J Cutler]

Momin,

That error message generally means what it says. There is no phenotype
present in the .fam file. You may notice there is also no sex information
present in the .fam file either (that's what the previous message means).

Edit your .fam file to include sex and phenotype and try again.

Cheers,
dave

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