Post date: Jun 09, 2017 7:7:5 PM
/uufs/chpc.utah.edu/common/home/u6013264/projects/lycaeides_wings/Gemma
scp u6013264@kingspeak.chpc.utah.edu:/uufs/chpc.utah.edu/common/home/u6013264/projects/lycaeides_wings/Gemma/output_all/genarch_all.txt ./
We have R code for making a plot that has PVE, PGE, n_gemma:
/uufs/chpc.utah.edu/common/home/u6000989/projects/lycaeides_wings/Gemma/scripts/barplot.R
pve = prop of pheno variance due to additive genetic effects (~heritability assuming you're picking up all causal loci; you are underestimating heritability if miss a causal locus; called "chip" heritability)
pge = % of pve due to SNPs with measurable effect
we are plotting pve (gray); pve*pge = % of the total variance due to SNP with measurable effect
change legend:
pve k + SNP
pve SNP
or
% var. explained k + SNP
% var. explained SNP
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anna results:
/uufs/chpc.utah.edu/common/home/u6000989/projects/lycaeides_wings/Gemma/output_grps/genarch_AN.txt
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all subgroups:
/uufs/chpc.utah.edu/common/home/u6000989/projects/lycaeides_wings/Gemma/output_grps/gen*