Quality control of dosage genotype matrix prior to LD calculation

LDqc(g, theta = 0.2, BestGuess = TRUE)

Arguments

g

NxM genotype score matrix for N individuals and M variants

theta

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

BestGuess

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"

Value

Outputs the "best guess" genotype matrix (if BestGuess=TRUE; default) or the "quality controlled" genotype matrix (if BestGuess=FALSE)

Author

Jenn Asimit