Closed zx8754 closed 4 years ago
w weight would be: 1/20000 ?
Yes
X ref is the panel genotype matrix with rows 20000 samples and columns 1000 SNPs?
Yes, and it should be column standardized (column mean 0, variance 1)
Why transpose and multiply X^T ref ?
This is how we compute sample correlation, X_ref^T X_ref / n_ref
What is z^T, how transposing a vector help?
z^T is the transpose of your z score vector. In the formula, we use z z^T, which is a matrix (1000 x 1000 matrix).
Do we need to set z_ld_weight = 1/100000, too?
No, z_ld_weight = 1/20000.
Your susie call should like
susie_rss(z=z, R=cor(X_ref), L=10, z_ld_weight=1/20000, estimate_residual_variance=T, estimate_prior_variance=T)
cor(X_ref) is the LD matrix, it is X_ref^T X_ref / (n_ref-1) with column-standardized X_ref. cor()
function will column-standardize X_ref for you.
@zouyuxin Thank you, this should get me going.
Struggling to understand the formula given to calculate R_ref in the manuals:
Could you clarify based on below settings I have:
Questions:
Apologies, probably missing basic understanding of how this package is supposed to work, appreciate any input. Thank you.