strataG (version 1.0.5)

lowFreqSubs: Low Frequency Substitutions

Description

Check nucleotide sites for low frequency substitutions.

Usage

lowFreqSubs(x, min.freq = 3, motif.length = 10, ...)

Arguments

x

a DNAbin object.

min.freq

minimum frequency of base to be flagged.

motif.length

length of motif around low frequency base to output.

...

arguments passed from other functions (ignored).

Value

data.frame listing id, site number, and motif around low frequency base call.

Examples

data(dolph.haps)
library(ape)

lowFreqSubs(as.DNAbin(dolph.haps))