Compute allele frequencies

get a vector of allele frequences from a dosage matrix

getAF(M)

Arguments

M

dosage matrix. Assumes SNPs in M coded 0, 1, 2 (requires rounding dosages to integers). M is Nind x Mrow, numeric matrix, with row/columanes to indicate SNP/ind ID

Value

vector of allele frequencies, names = SNP IDs if in cols of M

See also

Other helper: backsolveSNPeff(), centerDosage(), crosses2predict(), dose2domDevGenotypic(), dose2domDev(), effectsArray2list(), genmap2recombfreq(), genoVarCovarMatFunc(), getMAF(), getPropHom(), intensity(), kinship(), maf_filter(), quadform(), remove_invariant()