After running PLINK --lasso command with an h2 estimate 0.8, I received a plink.lasso; however, I am a little confused on how that file is supposed to be interpreted.
Here is a sample of the .lasso file:
And below is PLINK's .lasso documentation:
I understand that h2(heritability) relates to the measure of the influence genes may have on an individual, but how does that relate to the EFFECT column having negative values?
Could anyone clarify?
1 answer
i think the "effect" is something like beta in regression model, it estimate the effect A1 has to impact the phenotype value, like when performing TWAS , the phenotype is the gene expression, the effect tell you how large a SNP could influence the gene expression. And if the effect is negative, just like effect in GWAS, this allele have a negative effect on the phenotype value(larger A1 dosage, smaller phenotype value).
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