Why are there negative signed p-values in the PBAT output?

In Golden Helix SVS 6.3 there is an option under the PBAT Test Statistic and Computational tab to output "signed" p-values for SNP, haplotype and copy number analysis (Figure 1). Choosing this option will provide positive and negative p-values for the pvalue(FBAT) column in the output table.

NOTE: "Signed p-values" are only implemented for single phenotypes

What does the sign mean?

The sign is the sign of the sum of (phenotype - phenotypic mean) times ((marker score – expected marker score) given the parental genotypes) over all offspring (for trios, anyway).

If the sign of a "signed p-value" is positive, then the direction of the main effect is to make the phenotype more positive (or more likely to be a case) when the genotypic or haplotypic score or the intensity value is more positive, and the phenotype more negative (or less likely to be a case) when the genotypic or haplotypic score or the intensity value is more negative.

If the sign of a "signed p-value" is negative, then the direction of the main effect is to make the phenotype more negative (or less likely to be a case) when the genotypic or haplotypic score or the intensity value is more positive, and the phenotype more positive (or more likely to be a case) when the genotypic or haplotypic score or the intensity value is more negative.


Figure 1


Figure 2