Summary statistics

Calculates summary statistics useful for analyzing DNA.

## S3 method for class 'DNAmat_class'
summary(DNAmat)

Arguments

DNAmat	matrix; either a single-nucleotide polymorphism matrix or a segregating sites matrix of class 'DNAmat_class'.

Value

List containing the following components:

SFS

The site frequency spectrum

Watterson

Watterson's estimator.

pairwDiff

The pairwise difference estimator.

TajimaD

Tajima's D

See also

SFS, mutRate, TajimaD

Examples

# Using the function simDNAseq:
summary(simDNAseq(n = 12, seqLen = 20, mutRate = 5,
               popType = "varPop", expRate = 1.5))
#> Summary statistics:
#> Site frequency spectrum: 11 2 2 0 0 0 0 0 0 0 0 
#> Estimators of the scaled mutation rate:
#>  Watterson's estimator: 4.967089 
#>  Pairwise difference estimator: 3.257576 
#> Tajima's D: -1.477688 

# Creating a segregating sites matrix by hand:
DNAmat <- matrix(c(0,1,0,0,
                   0,1,0,1,
                   0,0,0,0,
                   0,0,0,0), 4,4, byrow=TRUE)
class(DNAmat) <- "DNAmat_class"
summary(DNAmat)
#> Summary statistics:
#> Site frequency spectrum: 1 1 0 
#> Estimators of the scaled mutation rate:
#>  Watterson's estimator: 1.090909 
#>  Pairwise difference estimator: 1.166667 
#> Tajima's D: 0.5915801