Help with PRS score

Question

[curious_butterfly]

Hello,

I've been struggling with constructing a PRS score. In the pics you can see how my summary stats and my target data look like.

Target Data:

Summary Stats:

I've tried the following code:

Rscript PRSice.R \
  --dir . \
  --prsice ./PRSice_linux \
  --base target \
  --target summary_stats.txt \
  --thread 1 \
  --stat BETA \
  --binary-target F

plink \
    --bfile target \
    --score summary_stats.txt 1 4 6 header \
    --out final

In both versions, it says no phenotypes found. I'm unsure what I'm doing wrong and would really appreciate some insight! Also, the data has been harmonized already so it should technically work!

[bk11]

Can you show how your target data .fam file looks like? What values are present in it's 6th column? Software is clearly stating you are missing phenotypes info in your fam file.

[curious_butterfly]

You're right! The values are -9 so they are missing. Do you know if there a way to calculate the PRS without the phenotype?

[bk11]

Is your data quantitative or binary? If it is quantitative, you should have NA instead of -9 in sixth column of your target data .fam file. Please check here.

[curious_butterfly]

the data is binary - but I can check if that helps just in case

[bk11]

Then why did you use --binary-target F if your data is binary. It should have been --binary-target TRUE. I would recommend to update phenotypes info in your target data and re-run PRSice with correct parameters.