filter a dosage matrix, removing invariant markers. Removes e.g. cases where MAF=0.5 but all dosages == 1 (het).
remove_invariant(M)
| 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 |
dosage matrix potentially with columns removed