Post by 183ttdtd on Oct 12, 2018 11:04:38 GMT
My apologies if I am posting a question that has been asked already.I have tried to search for the answer that may be helpful to me but I got more confused than I already was. So I was hoping it would be possible to help me directly.
I am very new to GCTA but from the papers that I have read, it sounds like a fascinating tool to master.
I have a continuous phenotype - adult height - not standardized measured in cm. I would like to find the estimated variance explained by my GWAS SNPs (over 1.3M).
I used the following line commands to achieve this:
./gcta_1.91.6beta/gcta64 --bfile my_data --autosome --maf 0.01 --make-grm --make-grm-gz --out my_data
./gcta64 --grm-gz my_data --grm-adj 0 --grm-cutoff 0.025 --make-grm --out my_data_adj
./gcta64 --reml --grm my_data_adj --pheno height.txt --reml-pred-rand --out my_data_adj_height
The results:
Source Variance SE
V(G) 32.694764 5.743938
V(e) 56.885691 5.648121
Vp 89.580454 1.541096
V(G)/Vp 0.364977 0.063192
logL -18739.697
logL0 -18758.033
LRT 36.672
df 1
Pval 6.9873e-10
n 6826
V(G) 32.694764 5.743938
V(e) 56.885691 5.648121
Vp 89.580454 1.541096
V(G)/Vp 0.364977 0.063192
logL -18739.697
logL0 -18758.033
LRT 36.672
df 1
Pval 6.9873e-10
n 6826
I have the following questions:
1) Are these commands accurate for the aim (I have been re-reading the description of all command provided. The description is very helpful, but I feel I might have misinterpret something)?
2) Is the variance explained by my SNPs 36.5% (SE=0.06)? (this bit is the most confusion for me as I am not sure which results is the actual variance explained of the phenotype)
3) is it normal for V(G), Ve and Vp to be beyond 0,1 range?
Thank you so much in advance. I will be very grateful for any comments and help with these questions.