strataG (version 1.0.5)

fixedDifferences: Fixed Differences

Description

Summarize fixed base pair differences between strata.

Usage

fixedDifferences(g, count.indels = TRUE, consec.indels.as.one = TRUE, bases = c("a", "c", "g", "t", "-"))

Arguments

g

a gtypes object.

count.indels

logical. Count indels when evaluating sites for fixed differences?

consec.indels.as.one

logical. If count.indels is TRUE, count consecutive indels as a a single indel?

bases

a character vector of valid bases to consider.

Value

a list with components:

See Also

fixedSites, variableSites

Examples

data(dloop.g)
fd <- fixedDifferences(dloop.g)
fd