regarding same PRS in one individual

[kayenat parveen]

Hello,

I used the PRSice-2 tool and found it very useful. However, I'm encountering some issues in the results that I don't fully understand. Could you please help me with this?  

My code is this;

#!/bin/bash

# Load R module
module purge
module load lang/R/4.2.2-foss-2022b

# Optional: Load any other dependencies if needed
# module load plink

# Define paths (update with your actual paths)
PRSICE_R="PRSice.R"
PRSICE_BIN="PRSice_linux"   # Use the correct binary for your system
BASE_FILE="02_NFL_4PRS_nameChange.txt"
TARGET_PREFIX="424_bfiles"  # PLINK files: target_genotypes.bed/bim/fam
PHENO_FILE="pheno.txt"
PHENO_COL="Z_score"
OUT_PREFIX="/PRS_test_NFL"

# Run PRSice-2
Rscript $PRSICE_R \
  --prsice $PRSICE_BIN \
  --base $BASE_FILE \
  --target $TARGET_PREFIX \
  --snp SNP \
  --chr CHR \
  --bp BP \
  --A1 A1 \
  --A2 A2 \
  --pvalue P \
  --score sum \
  --pheno $PHENO_FILE \
  --pheno-col $PHENO_COL \
  --stat BETA \
  --binary-target F \
  --no-full \
  --all-score\
  --out $OUT_PREFIX

------------------------------------

After performing this code, I got PRS for some of the individuals that were the same. For example;

Total number of participants: 424

153 individuals show 0 PRS

1 individual shows 0.058 PRS

199 individuals show 0.0726 PRS 

71 individuals show 0.1452 PRS.

Is it possible for 153, 199, or 71 individuals to have the same PRS value? PRS_test_NFL.summary

Phenotype       Set     Threshold       PRS.R2  Full.R2 Null.R2 Prevalence      Coefficient     Standard.Error      P       Num_SNP
-       Base    5e-08   0.00140038      0.00140038      0       -       -0.531469       0.690866   0.442156 1

  The results are a bit unclear to me. If you would like a log file, please let me know.