getSymbolFreqs.Sequence: Get a table with the frequencies of the states of a...

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Get a table with the frequencies of the states of a collection of Site objects aggregated by a Sequence object.

Usage

## S3 method for class 'Sequence'
getSymbolFreqs(this, index, ...)

Arguments

this	A Sequence object.
index	An integer vector specifying a set of positions. It is set to 1:seq$length if omitted.
...	Not used.

Value

A table.

Author(s)

Botond Sipos, Gregory Jordan

See Also

For more information see Sequence.

Examples

	# create a nucleotide sequence
	s<-NucleotideSequence(length=30,processes=list(list(JC69())))
	# sample states
	sampleStates(s)
	# get state frequencies from ranges 1:10 and 20:30
	getSymbolFreqs(s,c(1:10,20:30))
	# get symbol frequencies for the full sequence
	getSymbolFreqs(s)
 

phylosim documentation built on Nov. 22, 2019, 1:07 a.m.