Regarding --glm inetraction

[kayenat parveen]

Hello,

Greetings

I would like to run --glm interaction command from plink2 for checking the effect of Age in my analysis. I am not able to understand it properly. I have .pgen, .psam and .pvar files with phenotype and covariate files.

My covariates file : covar.txt

FID     IID     Age     sex     PC1     PC2     PC3     prmdiag
0       DE02GSADZND100207       76      f       -0.0031237      -0.105  -0.00975123     SCI
0       DE02GSADZND100304       76      m       -0.0142985      0.0102601       0.0202994       SCI

My phenotype file : pheno.txt

FID     IID     Z_score
0       DE16GSADZND100343       -0.771246613684981
0       DE12GSADZND100318       -0.609639897957642

My code for running interaction:

plink2 --pfile chr1_22 --pheno pheno.txt --pheno-name Z_score --glm genotypic interaction 'cols=+a1freq' hide-covar --ci 0.95 --covar covar.txt --covar-name Age,sex,PC1-PC3,prmdiag --covar-variance-standardize --maf 0.02 --out interaction_GWEIS

My result :

#CHROM  POS     ID      REF     ALT     A1      A1_FREQ TEST    OBS_CT  BETA    SE      L95     U95     T_OR_F_STAT     P       ERRCODE
1       727242  chr1:727242:G:A G       A       A       0.107375        ADD     275     NA      NA      NA      NA      NA      NA      CORR_TOO_HIGH
1       727242  chr1:727242:G:A G       A       A       0.107375        DOMDEV  275     NA      NA      NA      NA      NA      NA      CORR_TOO_HIGH

The result is not correct, as far as i understood. There is no p-value neither the effect size. Could you please let me know that how can i run the analysis correctly? I would like to show the interaction of snp with Age or with any other covariable. Please help me in this regard.

Thanking you in anticipation

Sincerely,

Kayenat Parveen