fixedDifferences: Fixed Differences

In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

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

Author(s)

Eric Archer <[e-mail]>

See Also

fixedSites, variableSites

Examples

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

EricArcher/strataG documentation built on Feb. 12, 2023, 4:11 a.m.