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haplotypes (version 1.1.2)

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

399

Version

1.1.2

License

GPL-2

Maintainer

Caner Aktas

Last Published

February 28th, 2020

Functions in haplotypes (1.1.2)

dna.obj

Example DNA sequence data
homopoly-methods

Provides the list of homoplastic indels and substitutions
remove.gaps-methods

Removing gaps from Dna object
image-methods

Display DNA Sequence
rownames-methods

Retrieve or set the row names
as.numeric-methods

Coerces a Dna object to a numeric matrix
haplotypes-internal

Internal function(s)
grouping-methods

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

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

Methods for function as.list in the Package haplotypes
as.networx-methods

Coerces an object to a networx object
basecomp-methods

Calculates base composition
tolower-methods, toupper-methods

Convert sequence characters from upper to lower case or vice versa
boot.dna-methods

Generates single bootstrap replicate
as.phyDat-methods

Coerces an object to a phyDat object
nrow-methods

Returns the number of DNA sequences
pairPhiST-methods

Provides the pairwise PhiST between populations
haplotypes-package

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

Extract Unique Sequences
ncol-methods

Returns the length of the longest DNA sequence
range-methods

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

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

Reorders haplotypes according to the ordering factor
length-methods

Methods for function length in the package haplotypes
distance-methods

Calculates absolute pairwise character difference matrix using a Dna object
names-methods

Function to get or set names of a Dna object or Parsimnet object
plot-methods

Methods for function plot in the package haplotypes
polymorp-methods

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

Estimates gene genealogies using statistical parsimony
pieplot-methods

Plots pie charts on statistical parsimony network
read.fas

Read sequences from a file in FASTA format
indelcoder-methods

Codes gaps
[-methods

Extract or replace parts of an object of class Dna
pielegend-methods

Add Legends to Plots
subs-methods

Displays base substitutions
show-methods

Methods for function show in the package haplotypes
as.data.frame-methods

Coerces a Dna object to a data.frame
Dna-class

Class "Dna" in the Package haplotypes
append-methods

Combines two Dna objects
Parsimnet-class

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

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

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

Coerces an object to a DNAbin object
as.matrix-methods

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

Class "Haplotype" in the Package haplotypes