strataG (version 1.0.3)

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))