LDqc.Rd
Quality control of dosage genotype matrix prior to LD calculation
LDqc(g, theta = 0.2, BestGuess = TRUE)
NxM genotype score matrix for N individuals and M variants
tolerance for dosage, e.g. if theta=0.2, then only dosages d that satisfy d<0.2, 0.8<d<1.2, and d>1.8 are retained
if TRUE, then return "best guess" genotype matrix (default); if FALSE, return dosage genotype matrix, where dosages that do not meet tolerance theta, are set to "NA"
Outputs the "best guess" genotype matrix (if BestGuess=TRUE; default) or the "quality controlled" genotype matrix (if BestGuess=FALSE)