Remove invariant SNPs from dosage matrix

filter a dosage matrix, removing invariant markers. Removes e.g. cases where MAF=0.5 but all dosages == 1 (het).

remove_invariant(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

thresh

threshold value. Columns of M with maf<thresh will be removed

Value

dosage matrix potentially with columns removed

See also

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