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.

Author
Caner Aktas
Date of publication
2015-04-26 09:49:28
Maintainer
Caner Aktas <caktas.aca@gmail.com>
License
GPL-2
Version
1.0
URLs

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'

Files in this package

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