strataG (version 1.0.3)

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: ll{ sites list of sites with fixed differences for each pair of strata num.fixed data.frame of number of sites fixed between each pair of strata }

See Also

fixedSites, variableSites