bnpsd (version 1.1.1)

fixed_loci: Identify fixed loci

Description

A locus is said to be 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. A locus with only missing elements (NA) will also be marked as fixed (TRUE). Below \(m\) is the number of loci, and \(n\) is the number of individuals.

Usage

fixed_loci(X)

Arguments

X

The \(m \times n\) genotype matrix

Value

A length-\(m\) boolean vector where the \(i\) element is TRUE if locus \(i\) is fixed or completely missing, FALSE otherwise.

Examples

# NOT RUN {
# 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)
)

# }