Identify fixed loci
A locus is "fixed" if the non-missing sub-vector contains all 0's or all 2's (the locus is completely homozygous for one allele or completely homozygous for the other allele).
This function tests each locus, returning a vector that is TRUE for each fixed locus, FALSE otherwise.
Loci with only missing elements (NA) are treated as fixed.
Below m is the number of loci, and n is the number of individuals.
fixed_loci(X)
X |
The |
A length-m boolean vector where the i element is TRUE if locus i is fixed or completely missing, FALSE otherwise.
# here's a toy genotype matrix
X <- matrix(
data = c(
2, 2, NA, # fixed locus (with one missing element)
0, NA, 0, # another fixed locus, for opposite allele
1, 1, 1, # NOT fixed (heterozygotes are not considered fixed)
0, 1, 2, # a completely variable locus
NA, NA, NA # completely missing locus (will be treated as fixed)
),
ncol = 3, byrow = TRUE)
# test that we get the desired values
stopifnot(
fixed_loci(X) == c(TRUE, TRUE, FALSE, FALSE, TRUE)
)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.