haplotypes: Haplotype Inference and Statistical Analysis of Genetic Variation

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>
http://cran.r-project.org, https://biolsystematics.wordpress.com/r/

View on CRAN

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'

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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