haplotypes: Haplotype Inference and Statistical Analysis of Genetic Variation
Version 1.0

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.

AuthorCaner Aktas
Date of publication2015-04-26 09:49:28
MaintainerCaner Aktas <caktas.aca@gmail.com>
LicenseGPL-2
Version1.0
URL http://cran.r-project.org https://biolsystematics.wordpress.com/r/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("haplotypes")

Getting started

Package overview

Popular man pages

append-methods: Combines two 'Dna' objects
distance-methods: Calculates absolute pairwise character difference matrix...
dna.obj: Example DNA sequence data
Haplotype-class: Class '"Haplotype"' in the Package 'haplotypes'
haplotype-methods: Methods for function 'haplotype' in the package 'haplotypes'
haplotypes-package: Haplotype inference and statistical analysis of genetic...
Parsimnet-class: Class '"Parsimnet"' in the Package 'haplotypes'
See all...

All man pages Function index File listing

Man pages

append-methods: Combines two 'Dna' objects
as.data.frame-methods: Coerces a 'Dna' object to a data.frame
as.dna-methods: Coerces an object to a 'Dna' object
as.list-methods: Methods for function 'as.list' in the Package 'haplotypes'
as.matrix-methods: Methods for function 'as.matrix' in the Package 'haplotypes'
as.numeric-methods: Coerces a 'Dna' object to a numeric matrix
distance-methods: Calculates absolute pairwise character difference matrix...
Dna-class: Class '"Dna"' in the Package 'haplotypes'
dna.obj: Example DNA sequence data
grouping-methods: Groups haplotypes according to the grouping variable...
Haplotype-class: Class '"Haplotype"' in the Package 'haplotypes'
haplotype-methods: Methods for function 'haplotype' in the package 'haplotypes'
haplotypes-internal: Internal function(s)
haplotypes-package: Haplotype inference and statistical analysis of genetic...
hapreord-methods: Reorders haplotypes according to the ordering factor
indelcoder-methods: Codes gaps
length-methods: Methods for function 'length' in the package 'haplotypes'
names-methods: Function to get or set names of a 'Dna' object
ncol-methods: Returns the length of the longest DNA sequence
nrow-methods: Returns the number of DNA sequences
pairnei-methods: Provides the average number of pairwise Nei's (D) differences...
Parsimnet-class: Class '"Parsimnet"' in the Package 'haplotypes'
parsimnet-methods: Estimates gene genealogies using statistical parsimony
plot-methods: Methods for function 'plot' in the package 'haplotypes'
polymorp-methods: Displays polymorphic sites (base substitutions and indels)...
read.fas: Read sequences from a file in FASTA format
show-methods: Methods for function 'show' in the package 'haplotypes'
subs-methods: Displays base substitutions
z[-methods: Extract or replace parts of an object of class 'Dna'

Functions

Files

inst
inst/example.fas
NAMESPACE
data
data/dna.obj.rda
R
R/classparsimnet.r
R/classhaplotype.r
R/classdna.r
MD5
DESCRIPTION
man
man/ncol-methods.Rd
man/plot-methods.Rd
man/polymorp-methods.Rd
man/distance-methods.Rd
man/hapreord-methods.Rd
man/z[-methods.Rd
man/as.numeric-methods.Rd
man/read.fas.Rd
man/haplotype-methods.Rd
man/dna.obj.Rd
man/nrow-methods.Rd
man/Haplotype-class.Rd
man/length-methods.Rd
man/names-methods.Rd
man/append-methods.Rd
man/as.matrix-methods.Rd
man/haplotypes-internal.Rd
man/as.dna-methods.Rd
man/as.list-methods.Rd
man/pairnei-methods.Rd
man/indelcoder-methods.Rd
man/subs-methods.Rd
man/haplotypes-package.Rd
man/grouping-methods.Rd
man/parsimnet-methods.Rd
man/as.data.frame-methods.Rd
man/Parsimnet-class.Rd
man/show-methods.Rd
man/Dna-class.Rd
haplotypes documentation built on May 19, 2017, 8:15 a.m.

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