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haplotypes (version 1.1.3)

Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony

Description

Provides S4 classes and methods for reading and manipulating aligned DNA sequences, supporting an indel coding methods (only simple indel coding method is available in the current version), showing base substitutions and indels, calculating absolute pairwise distances between DNA sequences, and collapses identical DNA sequences into haplotypes or inferring haplotypes using user provided absolute pairwise character difference matrix. This package also includes S4 classes and methods for estimating genealogical relationships among haplotypes using statistical parsimony and plotting parsimony networks.

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Version

Install

install.packages('haplotypes')

Monthly Downloads

451

Version

1.1.3

License

GPL-2

Maintainer

Caner Aktas

Last Published

June 29th, 2023

Functions in haplotypes (1.1.3)

as.list-methods

Methods for function as.list in the Package haplotypes
Haplotype-class

Class "Haplotype" in the Package haplotypes
dna.obj

Example DNA sequence data
as.data.frame-methods

Coerces a Dna object to a data.frame
as.network-methods

Coerces an object to a network object
as.phyDat-methods

Coerces an object to a phyDat object
distance-methods

Calculates absolute pairwise character difference matrix using a Dna object
boot.dna-methods

Generates single bootstrap replicate
basecomp-methods

Calculates base composition
grouping-methods

Groups haplotypes according to the grouping variable (populations, species, etc.)
hapreord-methods

Reorders haplotypes according to the ordering factor
haplotypes-package

Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony
names-methods

Function to get or set names of a Dna object or Parsimnet object
haplotypes-internal

Internal function(s)
nrow-methods

Returns the number of DNA sequences
pairPhiST-methods

Provides the pairwise PhiST between populations
ncol-methods

Returns the length of the longest DNA sequence
haplotype-methods

Methods for function haplotype in the package haplotypes
as.numeric-methods

Coerces a Dna object to a numeric matrix
as.networx-methods

Coerces an object to a networx object
indelcoder-methods

Codes gaps
parsimnet-methods

Estimates gene genealogies using statistical parsimony
pielegend-methods

Add Legends to Plots
polymorp-methods

Displays polymorphic sites (base substitutions and indels) between two sequences
plot-methods

Methods for function plot in the package haplotypes
pairnei-methods

Provides the average number of pairwise Nei's (D) differences between populations
remove.gaps-methods

Removing gaps from Dna object
image-methods

Display DNA Sequence
rownames-methods

Retrieve or set the row names
length-methods

Methods for function length in the package haplotypes
range-methods

Returns the minimum and maximum lengths of the DNA sequences
[-methods

Extract or replace parts of an object of class Dna
tolower-methods, toupper-methods

Convert sequence characters from upper to lower case or vice versa
read.fas

Read sequences from a file in FASTA format
unique-methods

Extract Unique Sequences
homopoly-methods

Provides the list of homoplastic indels and substitutions
pieplot-methods

Plots pie charts on statistical parsimony network
show-methods

Methods for function show in the package haplotypes
subs-methods

Displays base substitutions
as.DNAbin-methods

Coerces an object to a DNAbin object
append-methods

Combines two Dna objects
as.dna-methods

Coerces an object to a Dna object
Dna-class

Class "Dna" in the Package haplotypes
Parsimnet-class

Class "Parsimnet" in the Package haplotypes
as.matrix-methods

Methods for function as.matrix in the Package haplotypes