The function calculates the site frequency spectrum.
SFS(DNAmat)
| DNAmat | matrix; either a single-nucleotide polymorphism matrix or a segregating sites matrix. See details. |
|---|
The site frequency spectrum with class 'SFS_class'.
The site frequency spectrum is a vector of length \(n-1\), where \(n\) is the sample size. The \(i\)'th entry is the number of segregating sites where a mutation occur in \(i\) sequences.
The input to the function should be either a single-nucleotide polymorphism matrix or a segregating sites matrix. Either way, each row in the matrix represents a DNA sequence. The matrix should have a 1 where a mutation has occured and a 0 otherwise. If this is not the case, it will cause an error. If there exists a position on which all sequences have a mutation, it will cause a warning, and such a position will be treated as if it had no mutations.
#> [1] 2 0