Post by junjiao on Jun 28, 2017 2:41:05 GMT
Hi, jian
I have used GCTA-GREML to estimated the heritability of my trait, I used both genotyped data and imputed data, there are 101k SNPs in genotyped data, and 3015k SNPs in imputed data. and I used --grm-adj 0 to adjust estimates of genetic relationships, however ,I am confused with the results: the h2 estamited from the genotyped data is much large than the imputed data (h2=0.706198,SE= 0.333250; h2= 0.434212,SE=0.178918). So, what do you think about it ? Thank you for your help
this is the genotyped result:
Source Variance SE
V(G) 0.002898 0.001383
V(e) 0.001206 0.001364
Vp 0.004104 0.000162
V(G)/Vp 0.706198 0.333250
logL 2912.107
logL0 2909.885
LRT 4.444
df 1
Pval 0.01751
n 1309
this is the imputed result:
Source Variance SE
V(G) 0.001783 0.000746
V(e) 0.002323 0.000730
Vp 0.004107 0.000162
V(G)/Vp 0.434212 0.178918
logL 2910.261
logL0 2907.265
LRT 5.992
df 1
Pval 0.007187
n 1308
I have used GCTA-GREML to estimated the heritability of my trait, I used both genotyped data and imputed data, there are 101k SNPs in genotyped data, and 3015k SNPs in imputed data. and I used --grm-adj 0 to adjust estimates of genetic relationships, however ,I am confused with the results: the h2 estamited from the genotyped data is much large than the imputed data (h2=0.706198,SE= 0.333250; h2= 0.434212,SE=0.178918). So, what do you think about it ? Thank you for your help
this is the genotyped result:
Source Variance SE
V(G) 0.002898 0.001383
V(e) 0.001206 0.001364
Vp 0.004104 0.000162
V(G)/Vp 0.706198 0.333250
logL 2912.107
logL0 2909.885
LRT 4.444
df 1
Pval 0.01751
n 1309
this is the imputed result:
Source Variance SE
V(G) 0.001783 0.000746
V(e) 0.002323 0.000730
Vp 0.004107 0.000162
V(G)/Vp 0.434212 0.178918
logL 2910.261
logL0 2907.265
LRT 5.992
df 1
Pval 0.007187
n 1308
