strataG (version 1.0.3)

TiTvRatio: Transition / Transversion Ratio

Description

Calculate transition/transversion ratio. Test substitution type of two bases.

Usage

TiTvRatio(x)
subType(b1, b2)
isTi(b1, b2)
isTv(b1, b2)

Arguments

x

a gtypes object with aligned sequences or a list of aligned DNA sequences.

b1, b2

two bases to be compared.

Value

• TiTvRatio: a vector providing the number of transitions (Ti), transversions (Tv), and the transition/transversion ratio (Ti.Tv.ratio). subType: either "ti" for transition, or "tv" for transversion. isTi and isTv: a logical identifying whether the b1 to b2 is a transition or transversion.

Examples

data(dolph.seqs)

TiTvRatio(dolph.seqs)

subType("a", "c")

isTi("a", "c")

isTv("a", "c")