strataG (version 2.4.905)

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

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

# }