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strataG (version 2.0.2)

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:

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

Examples

Run this code
# NOT RUN {
data(dloop.g)
fd <- fixedDifferences(dloop.g)
fd

# }

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