Why does the P-value for ADD-INT_VAR sometimes become NA as shown below in the interaction testing results? Even in this case, the P-value for ADD-INT_SNPxVAR is output. Can this value be considered reliable?
CHROM GENPOS ID ALLELE0 ALLELE1 A1FREQ N TEST BETA SE CHISQ LOG10P EXTRA
10 122454735 DRAGEN:chr10:122454735:G:A G A 0.111759 2143 ADD 0.293981 0.10074 8.516 2.45341 NA
10 122454735 DRAGEN:chr10:122454735:G:A G A 0.111759 2143 ADD-INT_DRAGEN:chr1:196690107:C:T -0.988573 0.212356 21.6715 5.49004 NA
10 122454735 DRAGEN:chr10:122454735:G:A G A 0.111759 2143 ADD-INT_DRAGEN:chr1:196690107:C:T^2 -0.122955 0.0979164 1.57681 0.679396 NA
10 122454735 DRAGEN:chr10:122454735:G:A G A 0.111759 2143 ADD-INT_SNP 0.621651 0.207232 8.99873 2.56837 NA
10 122454735 DRAGEN:chr10:122454735:G:A G A 0.111759 2143 ADD-INT_SNPxDRAGEN:chr1:196690107:C:T -0.309019 0.170986 3.26624 1.15046 NA
10 122454735 DRAGEN:chr10:122454735:G:A G A 0.111759 2143 ADD-INT_2DF NA NA 10.7347 2.33101 NA
10 122454839 DRAGEN:chr10:122454839:C:T C T 0.145124 2143 ADD 0.267768 0.09152 8.56022 2.46396 NA
10 122454839 DRAGEN:chr10:122454839:C:T C T 0.145124 2143 ADD-INT_DRAGEN:chr1:196690107:C:T -0.997513 0.212271 NA NA NA <-- here
10 122454839 DRAGEN:chr10:122454839:C:T C T 0.145124 2143 ADD-INT_DRAGEN:chr1:196690107:C:T^2 -0.0927424 0.0984368 NA NA NA
10 122454839 DRAGEN:chr10:122454839:C:T C T 0.145124 2143 ADD-INT_SNP 0.865215 0.192421 20.2181 5.16056 NA
10 122454839 DRAGEN:chr10:122454839:C:T C T 0.145124 2143 ADD-INT_SNPxDRAGEN:chr1:196690107:C:T -0.472622 0.161961 9.1786 2.61108 NA
10 122454839 DRAGEN:chr10:122454839:C:T C T 0.145124 2143 ADD-INT_2DF NA NA 22.3526 4.85381 NA
10 122454932 DRAGEN:chr10:122454932:G:T G T 0.280915 2143 ADD -0.75721 0.0743687 103.67 23.6216 NA
10 122454932 DRAGEN:chr10:122454932:G:T G T 0.280915 2143 ADD-INT_DRAGEN:chr1:196690107:C:T -2.11371 0.26296 NA NA NA <-- here
10 122454932 DRAGEN:chr10:122454932:G:T G T 0.280915 2143 ADD-INT_DRAGEN:chr1:196690107:C:T^2 0.0646015 0.105821 NA NA NA
10 122454932 DRAGEN:chr10:122454932:G:T G T 0.280915 2143 ADD-INT_SNP -1.87392 0.141527 175.317 39.2921 NA
10 122454932 DRAGEN:chr10:122454932:G:T G T 0.280915 2143 ADD-INT_SNPxDRAGEN:chr1:196690107:C:T 0.985543 0.128073 62.025 14.4696 NA
10 122454932 DRAGEN:chr10:122454932:G:T G T 0.280915 2143 ADD-INT_2DF NA NA 198.134 43.0242 NA
An example of SNP combination that results in NA is shown below.There is no extreme skew in the phenotype or allele frequency.
pheno_gxg
DRAGEN:chr1:196690107:C:T DRAGEN:chr10:122454932:G:T 0 1
0 0 41 7
0 1 216 34
0 2 350 48
1 0 90 17
1 1 263 93
1 2 254 273
2 0 47 10
2 1 83 91
2 2 29 197
The command executed are as follows.
regenie --step 2 \
--pgen mypgen \
--ignore-pred \
--interaction-snp DRAGEN:chr1:196690107:C:T \
--interaction-file pgen,interaction_snps \
--phenoFile pheno.phe \
--covarFile pheno.phe \
--bt --approx --firth-se --firth \
--phenoCol pheno_gxg \
--bsize 200 \
--pThresh 0.05 \
--minMAC 3 \
--threads 16 \
--gz \
--out assoc
Why does the P-value for ADD-INT_VAR sometimes become NA as shown below in the interaction testing results? Even in this case, the P-value for ADD-INT_SNPxVAR is output. Can this value be considered reliable?
An example of SNP combination that results in NA is shown below.There is no extreme skew in the phenotype or allele frequency.
The command executed are as follows.