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haplotypes (version 1.0)

Haplotype Inference and Statistical Analysis of Genetic Variation

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 inferring haplotypes from DNA sequences or user provided absolute character difference matrix. This package also includes S4 classes and methods for estimating genealogical relationships among haplotypes using statistical parsimony.

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Version

Install

install.packages('haplotypes')

Monthly Downloads

398

Version

1.0

License

GPL-2

Homepage

http://cran.r-project.org

Maintainer

Caner Aktas

Last Published

April 26th, 2015

Functions in haplotypes (1.0)

Coerces an object to a Dna object

Parsimnet-class

Class "Parsimnet" in the Package haplotypes

hapreord-methods

Reorders haplotypes according to the ordering factor

haplotypes-package

Haplotype inference and statistical analysis of genetic variation

haplotypes-internal

Internal function(s)

parsimnet-methods

Estimates gene genealogies using statistical parsimony

Methods for function plot in the package haplotypes

distance-methods

Calculates absolute pairwise character difference matrix using a Dna object

polymorp-methods

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

Read sequences from a file in FASTA format

pairnei-methods

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

Example DNA sequence data

as.data.frame-methods

Coerces a Dna object to a data.frame

Returns the length of the longest DNA sequence

Displays base substitutions

as.matrix-methods

Methods for function as.matrix in the Package haplotypes

indelcoder-methods

Returns the number of DNA sequences

Combines two Dna objects

Extract or replace parts of an object of class Dna

Function to get or set names of a Dna object

Methods for function length in the package haplotypes

Haplotype-class

Class "Haplotype" in the Package haplotypes

Methods for function show in the package haplotypes

grouping-methods

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

as.list-methods

Methods for function as.list in the Package haplotypes

haplotype-methods

Methods for function haplotype in the package haplotypes

Class "Dna" in the Package haplotypes

as.numeric-methods

Coerces a Dna object to a numeric matrix