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xiaolei-lab / rMVP

:postbox: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool For Genome-Wide Association Study
Apache License 2.0
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Calculating PVE in rMVP #82

Open jhavill opened 1 year ago

jhavill commented 1 year ago

Hi Xiaolei,

GAPIT3 has the capacity to calculate the percent of phenotypic variation explained (PVE) by SNPs identified as significant in the GWAS.

Additionally, the results do not align with those identified in GAPIT (i.e. they produced different results).

How can one calculate the PVE from the model output and why do the results not align with GAPIT?

XiaoleiLiuBio commented 1 year ago

Hi Joshua,

For calculating the phenotypic variances or the genetic variances explained by top selected significant SNP, we have proposed a strategy in 2019, details please see https://www.frontiersin.org/articles/10.3389/fgene.2019.00302/full . Hope it helps.

Best, Xiaolei

---------- Origin message ----------

From："Joshua Havill" @.> To："xiaolei-lab/rMVP" @.> Subject：[xiaolei-lab/rMVP] Calculating PVE in rMVP (Issue #82) Date：2022-11-10 06:36:50Hi Xiaolei,

GAPIT3 has the capacity to calculate the percent of phenotypic variation explained (PVE) by SNPs identified as significant in the GWAS.

Additionally, the results do not align with those identified in GAPIT (i.e. they produced different results).

How can one calculate the PVE from the model output and why do the results not align with GAPIT?

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