Summary statistics needed for flashfm input
summaryStats(Xmat = TRUE, ybar.all, main.input)
| Xmat | logical, TRUE if main.input is based on genotype matrix (reference or from sample); FALSE if main.input based on covariance matrix |
|---|---|
| ybar.all | vector of trait means |
| main.input | output from flashfm.input |
list of 4 components: Mx = mean of SNPs, xcovo = covariance matrix of SNPs including column and row of 0s for intercept term, Sxy = matrix of Sxy values (column traits), ybar=vector of trait means