mutationSummary: Summary of observed mutations

In sidier: Substitution and Indel Distances to Infer Evolutionary Relationships

Description

This function computes the number of substitutions and indels observed in a given alignment.

Usage

mutationSummary(align, addExtremes = FALSE, output = "brief")

Arguments

align	the name of the "DNAbin" alignment to be analysed. See "?read.dna" in the ape package for details about reading alignments.
addExtremes	a logical; if TRUE, additional nucleotide sites are included in both extremes of the alignment. This will allow estimating distances for alignments showing gaps in terminal positions.
output	a string; defines the kind of output. Two values are accepted: - "brief" (default) produces an output showing the number of mutations (sites and events). - "detailed" produces an output showing the number of mutations (sites and events), the position of each mutation, and the state of these sites per sequence (A, T, C, G or - for substitutions and 1 or 0 for indels).

Value

A list containing:

Sites	A matrix containing: the number of sites per sequence (Length); the number of constant and variable sites; the number of singletons and informative sites.
Events	A matrix containing: the number of substitution (singletons, informative, and total) and indel (singletons, informative, and total) events
Constants.Alignment	A matrix showing constant sites in the alignment (Only shown if output=="detailed").
Variables.Alignment	A matrix showing variable sites in the alignment (Only shown if output=="detailed").
Singletons.Alignment	A matrix showing singleton sites in the alignment (Only shown if output=="detailed").
Inforatives.Alignment	A matrix showing informative sites in the alignment (Only shown if output=="detailed").
Substitutions	A matrix showing substitution sites in the alignment (Only shown if output=="detailed").
Subst.Single	A matrix showing singleton substitution sites in the alignment (Only shown if output=="detailed").
Subst.Info	A matrix showing informative substitution sites in the alignment (Only shown if output=="detailed").
Gaps	A matrix showing gap sites in the alignment (Only shown if output=="detailed").
Gaps.Single	A matrix showing singleton gap sites in the alignment (Only shown if output=="detailed").
Gaps.Info	A matrix showing informative gap sites in the alignment (Only shown if output=="detailed").

Author(s)

A. J. Muñoz-Pajares

Examples

# cat(">Population1_sequence1",
# "A-AGGGTC-CT---G",
# ">Population1_sequence2",
# "TAA---TCGCT---G",
# ">Population1_sequence3",
# "TAAGGGTCGCT---G",
# ">Population1_sequence4",
# "TAA---TCGCT---G",
# ">Population2_sequence1",
# "TTACGGTCG---TTG",
# ">Population2_sequence2",
# "TAA---TCG---TTG",
# ">Population2_sequence3",
# "TAA---TCGCTATTG",
# ">Population2_sequence4",
# "TTACGGTCG---TTG",
# ">Population3_sequence1",
# "TTA---TCG---TAG",
# ">Population3_sequence2",
# "TTA---TCG---TAG",
# ">Population3_sequence3",
# "TTA---TCG---TAG",
# ">Population3_sequence4",
# "TTA---TCG---TAG",
#      file = "ex3.fas", sep = "\n")
# 
# # Reading the alignment directly from file and saving no output file:
# library(ape)
# mutationSummary (align=read.dna("ex3.fas",format="fasta"))
# mutationSummary (align=read.dna("ex3.fas",format="fasta"),output="detailed")
# 
# #A more complex alignment
# data(ex_alignment1) # this will read a fasta file with the name 'alignExample'
# mutationSummary(align=alignExample,addExtremes=TRUE)
# 

sidier documentation built on June 25, 2021, 5:10 p.m.