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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
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