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.

Install the latest version of this package by entering the following in R:
install.packages("haplotypes")
AuthorCaner Aktas
Date of publication2015-04-26 09:49:28
MaintainerCaner Aktas <caktas.aca@gmail.com>
LicenseGPL-2
Version1.0
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'

Functions

alltest Man page
append Man page
append,Dna-method Man page
append-methods Man page
as.data.frame Man page
as.data.frame,Dna-method Man page
as.data.frame-methods Man page
as.dna Man page
as.dna,data.frame-method Man page
as.dna,Haplotype-method Man page
as.dna,list-method Man page
as.dna,matrix-method Man page
as.dna-methods Man page
as.list Man page
as.list,Dna-method Man page
as.list,Haplotype-method Man page
as.list-methods Man page
as.list,Parsimnet-method Man page
as.matrix Man page
as.matrix,Dna-method Man page
as.matrix-methods Man page
as.numeric Man page
as.numeric,Dna-method Man page
as.numeric-methods Man page
calcclust Man page
clustersG Man page
distance Man page
distance,Dna-method Man page
distance-methods Man page
Dna Man page
Dna-class Man page
[<-,Dna-method Man page
[,Dna-method Man page
dna.obj Man page
fillendgaps Man page
fillna Man page
grouping Man page
grouping,Haplotype-method Man page
grouping-methods Man page
haplo Man page
haplotype Man page
Haplotype Man page
Haplotype-class Man page
haplotype,dist-method Man page
haplotype,Dna-method Man page
haplotype,matrix-method Man page
haplotype-methods Man page
haplotypes Man page
haplotypes-package Man page
hapreord Man page
hapreord,Haplotype-method Man page
hapreord-methods Man page
indelcoder Man page
indelcoder,Dna-method Man page
indelcoder-methods Man page
initialize,Dna-method Man page
initialize,Haplotype-method Man page
initialize-methods Man page
initialize,Parsimnet-method Man page
length Man page
length,Dna-method Man page
length,Haplotype-method Man page
length-methods Man page
length,Parsimnet-method Man page
[-methods Man page
names Man page
names<-,Dna-method Man page
names,Dna-method Man page
names<--methods Man page
names-methods Man page
ncol Man page
ncol,Dna-method Man page
ncol-methods Man page
nrow Man page
nrow,Dna-method Man page
nrow-methods Man page
pairnei Man page
pairneidist Man page
pairnei,dist-method Man page
pairnei,Dna-method Man page
pairnei,matrix-method Man page
pairnei-methods Man page
parsimnet Man page
Parsimnet Man page
Parsimnet-class Man page
parsimnet,dist-method Man page
parsimnet,Dna-method Man page
parsimnet,matrix-method Man page
parsimnet-methods Man page
parsnet Man page
plot-methods Man page
plot,Parsimnet-method Man page
polymorp Man page
polymorp,Dna-method Man page
polymorp-methods Man page
read.fas Man page
recdistG Man page
show,Dna-method Man page
show,Haplotype-method Man page
show-methods Man page
show,Parsimnet-method Man page
sic Man page
steplimit Man page
subs Man page
subs,Dna-method Man page
subs-methods Man page
tryconnect Man page
tryconnectG Man page
validity Man page
xhaps Man page

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.