Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony

Description

This package 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 collapses identical DNA sequences into haplotypes or infering haplotypes using user provided absolute pairwise character difference matrix. This package also includes S4 classes and methods for estimating genealogical relationships among haplotypes using statistical parsimony and plotting parsimony networks.

Author(s)

Caner Aktas, caktas.aca@gmail.com

Examples

## Read example FASTA file.	
f<-system.file("example.fas",package="haplotypes") 
# invalid character 'N' was replaced with '?' with a warning message
x<-read.fas(file=f)
# an object of class 'Dna'
x 

## or load DNA Sequence data set.
data("dna.obj") 
x<-dna.obj
## Not run: 
x

## End(Not run)

## Compute an absolute pairwise character difference matrix from DNA sequences.
# coding gaps using simple indel coding method
d<- distance(x,indels="sic") 
## Not run: 
d

## End(Not run)

## Infer haplotypes using the 'Dna' object.
# coding gaps using simple indel coding method
h<-haplotype(x,indels="s") 
## Not run: 
h

## End(Not run)

## Conduct statistical parsimony analysis with 95% connection limit.
#algortihmic method
## Not run: 
p<-parsimnet(x,prob=.95) 
p
# plot network
plot(p) 

## End(Not run)

## Plotting pie charts on the statistical parsimony network
## Not run: 
data("dna.obj")
x<-dna.obj
h<-haplotypes::haplotype(x)

## Statistical parsimony with 95
p<-parsimnet(x) 

#randomly generated populations
pop<-c("pop1","pop2","pop3","pop4","pop5","pop6","pop7","pop8")
set.seed(5)
pops<-sample(pop,nrow(x),replace=TRUE)

# Plotting with default parameters.
pieplot(p,h,1, pops)


## End(Not run)

Class "Dna" in the Package haplotypes

Description

S4 class to hold DNA sequence data.

Objects from the Class

Objects can be created by calls of the form new("Dna", sequence, seqlengths, seqnames), however reading fasta file using read.fas function or coerce matrix, data.frame or list objects to a Dna object using as.dna methods is preferable.

Slots

sequence:

Object of class "matrix" containing DNA sequence data, rows represent sequences and columns represent sites. See also ‘Note’.

seqlengths:

Object of class "numeric" containing the length of each DNA sequence.

seqnames:

Object of class "character" containing the name of each DNA sequence.

Methods

[

signature(x = "Dna", i = "ANY", j = "ANY"): extracts part of a DNA sequence as an object of class matrix.

[<-

signature(x = "Dna", i = "ANY", j = "ANY", value = "ANY"): replaces part of a Dna sequence with an object of class "matrix", "numeric" or "character".

append

signature(x = "Dna", value = "ANY"): combines two Dna objects.

as.data.frame

signature(x = "Dna"): coerces an object of class Dna to a data.frame.

as.list

signature(x = "Dna"): coerces an object of class Dna to a list; elements of the list are character vectors that contains the DNA sequences of length equal to corresponding value in the slot seqlengths.

as.matrix

signature(x = "Dna"): coerces an object of class Dna to a matrix.

as.numeric

signature(x = "Dna"): coerces an object of class Dna to a numeric matrix.

as.DNAbin

signature(x = "Dna"): coerces an object of class Dna to a DNAbin object.

as.phyDat

signature(x = "Dna"): coerces an object of class Dna to a phyDat object.

basecomp

signature(x = "Dna"): calculates base composition of Dna object.

boot.dna

signature(x = "Dna"): generates single bootstrap replicate.

distance

signature(x = "Dna"): computes and returns an absolute pairwise character difference matrix from DNA sequences.

haplotype

signature(x = "Dna"): infers haplotypes from DNA sequences.

image

signature(x = "Dna"): displays DNA sequences

indelcoder

signature(x = "Dna"): supports simple indel coding method.

length

signature(x = "Dna"): returns the longest sequence length.

append

signature(x = "Dna", value = "ANY"): combines two Dna objects.

names

signature(x = "Dna"): gets the names of an object Dna.

names<-

signature(x = "Dna"): sets the names of an object Dna.

ncol

signature(x = "Dna"): returns the longest sequence length.

nrow

signature(x = "Dna"): returns the total sequence number.

pairnei

signature(x = "Dna"): calculates pairwise Nei's average number of differences between populations.

pairPhiST

signature(x = "Dna"): calculates pairwise PhiST between populations.

parsimnet

signature(x = "Dna"): estimates genealogies using statistical parsimony.

polymorp

signature(x = "Dna"): displays information about DNA polymorphisms of two sequences; indels and base substitutions, respectively.

range

signature(object = "Dna"): returns a vector containing the minimum and maximum length of DNA sequences.

remove.gaps

signature(object = "Dna"): removes alignment gaps.

rownames

signature(object = "Dna"): retrieve the row names of a DNA sequence matrix.

rownames<-

signature(object = "Dna"): set the row names of a DNA sequence matrix.

show

signature(object = "Dna"): displays Dna object briefly.

subs

signature(x = "Dna"): displays information about base substitutions.

tolower

signature(x = "Dna"): Translate characters in DNA sequence matrix from upper to lower case.

toupper

signature(x = "Dna"): Translate characters in DNA sequence matrix from lower to upper case.

unique

signature(x = "Dna"): returns a list with duplicate DNA sequences removed.

Note

Valid characters for the slot sequence are "A","C","G","T","a","c","g","t","-","?". Numeric entries (integers) between 0-5 will be converted to "?","A","C","G","T","-", respectively. Invalid characters will be replaced with "?" with a warning message.

Author(s)

Caner Aktas, caktas.aca@gmail.com

Class "Haplotype" in the Package haplotypes

Description

S4 class to store haplotype information.

Objects from the Class

Objects can be created by calls of the form new("Haplotype", haplist, hapind, uniquehapind, sequence, d, freq, nhap), however use function haplotype instead.

Slots

haplist:

Object of class "list", containing the names of individuals that share the same haplotype.

hapind:

Object of class "list", containing the index of individuals that share the same haplotype.

uniquehapind:

Object of class "numeric", containing the index of the first occurrence of unique haplotypes.

sequence:

Object of class "matrix" if present, giving the DNA sequence matrix of unique haplotypes.

d:

Object of class "matrix", giving the absolute pairwise character difference matrix of unique haplotypes.

freq:

Object of class "numeric", giving the haplotype frequencies.

nhap:

Object of class "numeric", giving the total number of haplotypes.

Methods

as.dna

signature(x = "Haplotype"): if Haplotype object contains dna sequences, coerces an object of class Haplotype to an object of class Dna, else returns an error message.

as.list

signature(x = "Haplotype"): assigns slots of an object Haplotype to list elements.

grouping

signature(x = "Haplotype"): creates a matrix with haplotypes as rows, grouping factor (populations, species, etc.) as columns and abundance as entries.

hapreord

signature(x = "Haplotype"): reorders haplotypes according to the ordering factor.

length

signature(x = "Haplotype"): returns the number of haplotypes.

pieplot

signature(x = "Parsimnet", y = "Haplotype"): plot pie charts on statistical parsimony network.

pielegend

signature(x = "Parsimnet", y = "Haplotype"): add legends to pie charts produced using pieplot.

show

signature(object = "Haplotype"): displays the object briefly.

Author(s)

Caner Aktas, caktas.aca@gmail.com

Class "Parsimnet" in the Package haplotypes

Description

S4 class to store statistical parsimony networks and additional information.

Objects from the Class

Objects can be created by calls of the form new("Parsimnet", d, tempProbs, conlimit, prob, nhap, rowindex), however use function parsimnet instead.

Slots

d:

Object of class "list" containing the geodesic distance matrix of haplotypes and intermediates for each network.

tempProbs:

Object of class "numeric" giving the probabilities of parsimony for mutational steps beyond the connection limit.

conlimit:

Object of class "numeric" giving the number of maximum connection steps at connection limit.

prob:

Object of class "numeric" giving the user defined connection limit.

nhap:

Object of class "numeric" giving the number of haplotypes in each network.

rowindex:

Object of class "list" containing vectors giving the index of haplotypes in each network.

Methods

as.list

signature(x = "Parsimnet"): assigns slots of an object Parsimnet to list elements.

as.network

signature(x = "Parsimnet"): coerces Parsimnet object to network {network} object

as.networx

signature(x = "Parsimnet"): coerces Parsimnet object to networx {phangorn} object

length

signature(x = "Parsimnet"): returns the length of network(s).

names

signature(x = "Parsimnet"): gets names of networks in Parsimnet object

names<-

signature(x = "Parsimnet"): sets names of networks in Parsimnet object

plot

signature(x = "Parsimnet"): plots statistical parsimony networks.

pieplot

signature(x = "Parsimnet", y = "Haplotype"): plots pie charts on statistical parsimony networks

pielegend

signature(x = "Parsimnet", y = "Haplotype"): add legends to pie charts produced using pieplot.

rownames

signature(x = "Parsimnet"): gets names of vertices in networks.

rownames<-

signature(x = "Parsimnet"): gets names of vertices in networks

show

signature(object = "Parsimnet"): displays the object briefly.

Author(s)

Caner Aktas, caktas.aca@gmail.com

Extract or replace parts of an object of class Dna

Description

Operators acting on sequence matrix to extract or replace parts.

Usage

## S4 method for signature 'Dna'
x[i, j,..., drop = FALSE]
## S4 replacement method for signature 'Dna'
x[i, j]<- value

Arguments

Details

The S4 method dispatch mechanism matches arguments based on those specified in the signature of the corresponding generic function. However, for some generics that include '...' in their signature, additional arguments can be incorporated in specific methods. Notably, the '[' function does not follow this pattern and restricts the arguments to those defined in its signature. In this context, the 'as.matrix' argument is not in the signature of the generic '[', so it is included within '...'. Then, within the body of the function, we check whether 'as.matrix' has been provided in the actual arguments when the function is called. If 'as.matrix' is not specified, the function defaults to 'TRUE', preserving the behavior of previous versions of the method.

Value

returns an object of class matrix, vector or Dna.

Methods

signature(x = "Dna", i = "ANY", j = "ANY", drop = "ANY")

Author(s)

Caner Aktas, caktas.aca@gmail.com

See Also

Dna

Examples

data("dna.obj")
x<-dna.obj

## Extract parts.
# a matrix object
x[1:2,1:3]

# a Dna object, as.dna(x[1:2,1:3]) gives the same result
x[1:2,1:3,as.matrix=FALSE] 

# a vector object
x[1,1:4,drop=TRUE]

## Replace parts.
#"G" "C"
x[1,1:2] 	
x[1,1:2]<-c("A","T")
x[1,1:2]

Combines two Dna objects

Description

Combines two Dna objects.

Usage

## S4 method for signature 'Dna'
append(x,values)

Arguments

Value

an object of class Dna.

Methods

signature(x = "Dna", values= "Dna")

combines two Dna objects.

Examples

	
data("dna.obj")

x<-dna.obj
y<-dna.obj
nrow(x)

## Combining two 'Dna' objects.
z<- append(x,y)
nrow(z)

Coerces an object to a DNAbin object

Description

This function coerces Dna object to DNAbin {ape} object .

Usage

## S4 method for signature 'Dna'
as.DNAbin(x, endgaps=TRUE)

Arguments

Value

an object of class DNAbin.

Methods

signature(x = "Dna")

coerces a Dna object to a DNAbin object.

Examples

## Coercing a Dna object to a DNAbin object.
data("dna.obj")

x<-dna.obj
dBin<-as.DNAbin(x)
dBin

#gaps at the end removed
dBin<-as.DNAbin(x, endgaps=FALSE)
dBin

Coerces a Dna object to a data.frame

Description

Coerces an object to a data.frame.

Usage

## S4 method for signature 'Dna'
as.data.frame(x)

Arguments

Value

returns a data frame.

Methods

signature(x = "Dna")

coerces a Dna object to a data.frame.

Examples

data("dna.obj")

x<-dna.obj
x<-as.dna(x[1:4,1:6])

## Coercing a 'Dna' object to a data.frame.
df<-as.data.frame(x)
df

# TRUE
is.data.frame(df) 

## Not run: 
# gives the same result 
df<-as.data.frame(x@sequence) 
df

## End(Not run)

Coerces an object to a Dna object

Description

Coerces an object that contains DNA sequences to an object of Class Dna.

Usage

## S4 method for signature 'matrix'
as.dna(x)
## S4 method for signature 'data.frame'
as.dna(x)
## S4 method for signature 'list'
as.dna(x)
## S4 method for signature 'character'
as.dna(x)
## S4 method for signature 'Haplotype'
as.dna(x)
## S4 method for signature 'DNAbin'
as.dna(x)
## S4 method for signature 'phyDat'
as.dna(x)

Arguments

Details

Elements of the list must be vectors. Each element of the list contains a single DNA sequence. If the sequence lengths differ, the longest sequence is taken into account and gaps are introduced to the shorter sequences at the end of the matrix in the slot sequence. Sequence length information is stored in the slot seqlengths.

Valid characters for the slot sequence are "A","C","G","T","a","c","g","t","-","?". During the conversion of the object to the class Dna, integers 0,1,2,3,4,5 or characters "0","1","2","3","4","5" are converted to "?","A","C","G","T","-", respectively. Invalid characters are replaced with "?" with a warning message.

Value

an object of class Dna.

Methods

signature(x = "matrix")

coerces matrix to a Dna object.

signature(x = "data.frame")

coerces data.frame to a Dna object.

signature(x = "list")

coerces list to a Dna object.

signature(x = "character")

coerces characters to a Dna object.

signature(x = "Haplotype")

coerces a Haplotype object to a Dna object.

signature(x = "DNAbin")

coerces a DNAbin object to a Dna object.

signature(x = "phyDat")

coerces a phyDat object to a Dna object.

Examples

## Coercing a matrix to a 'Dna' object.
# all valid characters
x<-matrix(c("?","A","C","g","t","-","0","1","2","3","4","5"),4,6)
rownames(x)<-c("seq1","seq2","seq3","seq4") 
dna.obj<-as.dna(x) 
dna.obj
# the sequence matrix
dna.obj@sequence

## Not run: 
# includes invalid characters
x<-matrix(c("X","y","*","?","t","-","0","1","2","3","4","5"),4,6) 
rownames(x)<-c("seq1","seq2","seq3","seq4") 
dna.obj<-as.dna(x) 
dna.obj
dna.obj@sequence

# all valid integers
x<-matrix(c(0,1,2,3,4,5,0,1,2,3,4,5),4,6) 
rownames(x)<-c("seq1","seq2","seq3","seq4") 
dna.obj<-as.dna(x) 
dna.obj
dna.obj@sequence

## Coercing a data.frame to a 'Dna' object.
x<-data.frame(matrix(c("?","A","C","g","t","-","0","1","2","3","4","5"),4,6)) 
rownames(x)<-c("seq1","seq2","seq3","seq4") 
dna.obj<-as.dna(x) 
dna.obj
dna.obj@sequence

## Coercing a list to a 'Dna' object.
seq1<-c("?","A","C","g","t","-","0","1")
seq2<-c("?","A","C","g","t","-","0","1","2")
seq3<-c("?","A","C","g","t","-","0","1","2","3")
x<-list(seq1=seq1,seq2=seq2,seq3=seq3) 
dna.obj<-as.dna(x)

# sequence lengths differ 
dna.obj@seqlengths
dna.obj@sequence

## Coercing a character vector to a Dna object.
seq<-c("?","A","C","g","t","-","0","1")
x<-as.dna(seq)
x


## Coercing a Haplotype object to a Dna object.
data("dna.obj")
x<-dna.obj
h<-haplotype(x)

# DNA Sequences of unique haplotypes  
dna.obj<-as.dna(h)
dna.obj

d<-distance(x)

# if 'Haplotype' object does not contain 'DNA' Sequences
h<-haplotype(d)

# returns an error
as.dna(h)

## Coercing a DNAbin object to a Dna object.
require(ape)
data(woodmouse)
x<-as.dna(woodmouse)
x


## End(Not run)

Methods for function as.list in the Package haplotypes

Description

Coerces an object to a list.

Usage

## S4 method for signature 'Dna'
as.list(x)
## S4 method for signature 'Haplotype'
as.list(x)
## S4 method for signature 'Parsimnet'
as.list(x)

Arguments

Details

If x is a Dna object, elements of the list are character vectors that contains the DNA sequences of length equal to corresponding value in the slot seqlengths. If x is Haplotype or Parsimnet objects, slots are converted to list elements.

Value

returns a list.

Methods

signature(x = "Dna")

coerces an object of class Dna to a list.

signature(x = "Haplotype")

coerces an object of class Haplotype to a list.

signature(x = "Parsimnet")

coerces an object of class Parsimnet to a list.

Examples

data("dna.obj")

## Coercing a 'Dna' object to a list.
x<-dna.obj[1:3,as.matrix=FALSE]
as.list(x)

## Not run: 
## Coercing a 'Haplotype' object to a list.
x<-dna.obj
h<-haplotype(x)
as.list(h)

## Coercing a 'Parsimnet' object to a list.
x<-dna.obj
p<-parsimnet(x)
as.list(p)

## End(Not run)

Methods for function as.matrix in the Package haplotypes

Description

Coerces an object to a matrix.

Usage

## S4 method for signature 'Dna'
as.matrix(x)

Arguments

Value

returns a character matrix.

Methods

signature(x = "Dna")

coerces an object of class Dna to a matrix.

Examples

data("dna.obj")

## Coercing a 'Dna' object to a matrix.
x<-dna.obj[1:4,1:6,as.matrix=FALSE]
x
as.matrix(x)

## Not run: 
# gives the same result
dna.obj[1:4,1:6,as.matrix=TRUE] 
## End(Not run)

Coerces an object to a network object

Description

This function coerces Parsimnet object to network {network} object .

Usage

## S4 method for signature 'Parsimnet'
as.network(x,net=1,...)

Arguments

Value

an object of class network.

Methods

signature(x = "Parsimnet")

coerces a Parsimnet object to a network object.

Examples

## Coercing a Parsimnet object to a network object.
data("dna.obj")
x<-dna.obj
p<-parsimnet(x)
n<-as.network(p)

#Fourth network (with only two edges)
p<-parsimnet(x,prob=.99)
n<-as.network(p,net=4)

Coerces an object to a networx object

Description

This function coerces Parsimnet object to networx {phangorn} object .

Usage

## S4 method for signature 'Parsimnet'
as.networx(x,net=1,...)

Arguments

Value

an object of class networx.

Methods

signature(x = "Parsimnet")

coerces a Parsimnet object to a networx object.

Examples

## Coercing a Parsimnet object to a networx object.
data("dna.obj")
x<-dna.obj
p<-parsimnet(x)
nx<-as.networx(p)
plot(nx, "2D")

Coerces a Dna object to a numeric matrix

Description

Converts a character matrix to a numeric matrix.

Usage

## S4 method for signature 'Dna'
as.numeric(x)

Arguments

Details

Function as.numeric() coerces the character matrix in the slot sequence to a numeric matrix. Lower or upper case characters "?","A","C","G","T","-" are converted to integers 0,1,2,3,4,5, respectively.

Value

returns a numeric matrix.

Methods

signature(x = "Dna")

coerces a Dna object to a numeric matrix.

Examples

x<-matrix(c("?","A","C","g","t","-","0","1","2","3","4","5"),4,6)
rownames(x)<-c("seq1","seq2","seq3","seq4") 
x<-as.dna(x)
# original character matrix 
as.matrix(x) 

## Coercing a 'Dna' object to a numeric matrix.
# numeric matrix
as.numeric(x)

Coerces an object to a phyDat object

Description

This function coerces Dna object to phyDat {phangorn} object .

Usage

## S4 method for signature 'Dna'
as.phyDat(x, indels="sic",...)

Arguments

Details

Available indel coding methods:

sic:

Treating gaps as a missing character and coding them separately following the simple indel coding method.

5th:

Treating gaps as a fifth state character.

missing:

Treating gaps as a missing character.

Value

an object of class phyDat.

Methods

signature(x = "Dna")

coerces a Dna object to a phyDat object.

Examples

data("dna.obj")
x<-dna.obj


## Coercing a Dna object to a phyDat object.
# Simple indel coding.
phyd<-as.phyDat(x)
phyd

# Gaps as 5th state characters.
phyd<-as.phyDat(x,indels="5")
phyd

# Gaps as 5th state characters.
phyd<-as.phyDat(x,indels="m")
phyd

Calculates base composition

Description

Calculates base composition of Dna object.

Usage

## S4 method for signature 'Dna'
basecomp(x)

Arguments

Value

a matrix with sequence as rows, DNA bases as columns and frequencies as entries.

Methods

signature(x = "Dna")

calculates base composition of Dna object.

Examples

data("dna.obj")
x <-dna.obj

## Calculating base compositions.
basecomp(x)

Generates single bootstrap replicate

Description

Methods for generating a single bootstrap replicate.

Usage

## S4 method for signature 'Dna'
boot.dna(x,replacement=TRUE)

Arguments

Value

an object of class Dna.

Methods

signature(x = "Dna")

generates single bootstrap replicate from a Dna object.

Author(s)

Caner Aktas, caktas.aca@gmail.com

Examples

	
	
data("dna.obj")
x<-dna.obj

## Generating a bootstrap replicate.
# with replacement
bxr<-boot.dna(x)
image(bxr)

# without replacement
bx<-boot.dna(x,replacement=FALSE)
image(bx)

Calculates absolute pairwise character difference matrix using a Dna object

Description

Computes and returns an absolute pairwise character difference matrix from DNA sequences.

Usage

## S4 method for signature 'Dna'
distance(x,subset=NULL,indels="sic")

Arguments

Details

Available indel coding methods:

sic:

Treating gaps as a missing character and coding them separately following the simple indel coding method.

5th:

Treating gaps as a fifth state character.

missing:

Treating gaps as a missing character.

Value

returns an object of class dist.

Methods

signature(x = "Dna")

Computes and returns an absolute pairwise character difference matrix from Dna objects.

Author(s)

Caner Aktas, caktas.aca@gmail.com

References

Giribet, G. and Wheeler, W.C. (1999) On gaps. Molecular Phylogenetics and Evolution 13, 132-143.

Simmons, M., Ochoterena, H. (2000) Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49, 369-381.

See Also

indelcoder and subs

Examples

data("dna.obj")
x<-dna.obj[4:7,13:22,as.matrix=FALSE]

## Simple indel coding.
distance(x,indels="s")

## Gaps as 5th state characters.
distance(x,indels="5")

## Gaps as missing characters.
distance(x,indels="m")

## Not run: 
## Using 'subset'.
x<-dna.obj[4:10,13:22,as.matrix=FALSE]
distance(x, NULL)
distance(x, subset=c(1))
distance(x, subset=c(2,4))

## End(Not run)

Example DNA sequence data

Description

An example object of the class Dna.

Usage

data(dna.obj)

Format

dna.obj contains a Dna object.

Examples

data(dna.obj)
dna.obj

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

Description

Function for creating a matrix with haplotypes as rows, grouping factor (populations, species, etc.) as columns and abundance as entries.

Usage

## S4 method for signature 'Haplotype'
grouping(x,factors)

Arguments

Value

a list with two components:

hapmat:

a matrix with haplotypes as rows, levels of the grouping factor (populations, species, etc.) as columns and abundance as entries.

hapvec:

a vector giving the haplotype identities of individuals.

Methods

signature(x = "Haplotype")

Author(s)

Caner Aktas, caktas.aca@gmail.com

See Also

haplotype

Examples

data("dna.obj")
x<-dna.obj[1:6,,as.matrix=FALSE]
# inferring haplotypes from DNA sequences
h<-haplotype(x) 

## Grouping haplotypes.
# character vector 'populations' is a grouping factor.
populations<-c("pop1","pop1","pop2","pop3","pop3","pop3") 

# length of the argument 'factor' is equal to the number of sequences
g<-grouping(h,factors=populations) 
g

Methods for function haplotype in the package haplotypes

Description

Collapses identical DNA sequences into haplotypes or infering haplotypes using user provided absolute pairwise character difference matrix.

Usage

## S4 method for signature 'Dna'
haplotype(x,indels="sic")
## S4 method for signature 'dist'
haplotype(x)
## S4 method for signature 'matrix'
haplotype(x)

Arguments

Value

haplotype returns an object of class Haplotype, as.list-methods can be used to coerce the object to a list.

Methods

signature(x = "Dna")

Inferring haplotypes from DNA sequences.

signature(x = "dist")

Inferring haplotypes using an absolute pairwise character difference matrix (dist object).

signature(x = "matrix")

Inferring haplotypes using an absolute pairwise character difference matrix.

Author(s)

Caner Aktas, caktas.aca@gmail.com

Examples

	
data("dna.obj")
x<-dna.obj[1:6,,as.matrix=FALSE]

##Inferring haplotypes using 'Dna' object.
# coding gaps using simple indel coding method
h<-haplotype(x,indels="sic")
h

# giving DNA sequences of haplotypes
as.dna(h) 

## Not run: 
	
## Slots of an object Haplotype	
h@haplist  #haplotype list (names)
h@hapind  #haplotype list (index)
h@uniquehapind  #getting index of the first occurrence of haplotypes
h@sequence  #DNA sequences of haplotypes
h@d  #distance matrix of haplotypes
h@freq  #haplotype frequencies
h@nhap  #total number of haplotypes

## End(Not run)

## Inferring haplotypes using dist object. 
d<-distance(x)
h<-haplotype(d) 
h
## Not run: 
# returns an error message 
as.dna(h)

## End(Not run) 

## Inferring haplotypes using distance matrix.
d<-as.matrix(distance(x))
h<-haplotype(d) 
h
## Not run: 
# returns an error message
as.dna(h)

## End(Not run)  

Internal function(s)

Description

Internal function(s)

Reorders haplotypes according to the ordering factor

Description

Reorders haplotypes according to the ordering factor.

Usage

## S4 method for signature 'Haplotype'
hapreord(x,order=c(1:x@nhap))

Arguments

Value

returns an object of class Haplotype.

Methods

signature(x = "Haplotype")

Reorders haplotypes.

Author(s)

Caner Aktas, caktas.aca@gmail.com

See Also

haplotype

Examples

data("dna.obj")
x<-dna.obj[1:6,,as.matrix=FALSE]
# inferring haplotypes from DNA sequences
h<-haplotype(x)

## Reordering haplotypes.

# length of the argument 'order' is equal to the number of haplotypes
rh<-hapreord(h,order=c(4,3,1,2))
rh

Provides the list of homoplastic indels and substitutions

Description

This function returs the list of homoplastic indels and substitutions.

Usage

## S4 method for signature 'Dna'
homopoly(x,indels="sic",...)

Arguments

Value

a list with following components:

Methods

signature(x = "Dna")

Author(s)

Caner Aktas, caktas.aca@gmail.com

Examples

data("dna.obj")

### Method for signature 'Dna'.
x<-dna.obj
homopoly(x)

Display DNA Sequence

Description

Display an image of DNA sequences .

Usage

## S4 method for signature 'Dna'
image(x,all=FALSE,fifth=TRUE,
col=c("#BFBFBF","#0B99FD","#FD0B0B","#11A808","#F5FD0B","#F8F8FF"),
chars=TRUE,cex=1,show.names=TRUE,show.sites=TRUE,xlab="",ylab="",...)
 

Arguments

Methods

signature(x = "Dna")

Display an image of Dna objects

Author(s)

Caner Aktas, caktas.aca@gmail.com.

See Also

image.default

Examples

data("dna.obj")
x<-dna.obj

## Display only polymorphic sites without gaps
image(x,all=FALSE,fifth=FALSE,show.names=TRUE,cex=0.6)

## Display only polymorphic sites with gaps
image(x,all=FALSE,fifth=TRUE,show.names=TRUE,cex=0.6)

## Not run: 
## Display entire sequences
image(x,all=FALSE,show.names=TRUE,cex=0.6)

## End(Not run)

Codes gaps

Description

Function for coding gaps separately. Only simple indel coding method is available in the current version.

Usage

## S4 method for signature 'Dna'
indelcoder(x)

Arguments

Value

a list with two components:

indels:

a matrix giving the indel positions (beginnings and ends) and lengths.

codematrix:

a binary matrix giving the indel codings. Missing values are denoted by -1.

Methods

signature(x = "Dna")

Function for coding gaps separately.

Author(s)

Caner Aktas, caktas.aca@gmail.com

References

Simmons, M., Ochoterena, H. (2000) Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49, 369-381.

See Also

distance

Examples

data("dna.obj")
x<-dna.obj

## Simple indel coding.
indelcoder(x)

Methods for function length in the package haplotypes

Description

Methods for function length.

Usage

## S4 method for signature 'Dna'
length(x)
## S4 method for signature 'Haplotype'
length(x)
## S4 method for signature 'Parsimnet'
length(x)

Arguments

Value

returns a non-negative integer vector.

Methods

signature(x = "Dna")

returns the longest sequence length.

signature(x = "Haplotype")

returns the number of haplotypes.

signature(x = "Parsimnet")

returns the length of network(s).

See Also

ncol-methods

Examples

data("dna.obj")
x<-dna.obj

## Longest sequence length
length(x)


## Total number of haplotypes
h<-haplotype(x)
length(h)

## Length of network(s)
p<-parsimnet(x,prob=.95)
# length of the network
length(p)
 
p<-parsimnet(x,prob=.99)
# length of the networks
length(p)

Function to get or set names of a Dna object or Parsimnet object

Description

Function to get or set sequence names of Dna object or names of network in Parsimnet object.

Usage

## S4 method for signature 'Dna'
names(x)
## S4 method for signature 'Parsimnet'
names(x)
## S4 replacement method for signature 'Dna'
names(x)<-value
## S4 replacement method for signature 'Parsimnet'
names(x)<-value

Arguments

Methods

signature(x = "Dna")

Function to get or set names of an object of Dna.

signature(x = "Parsimnet")

Function to get or set names of networks in Parsimnet object.

Examples

data("dna.obj")

x<-dna.obj
x<-as.dna(x[1:4,1:6])

## Getting sequence names.
names(x)

## Setting sequence names.
names(x)<-c("u","v","z","y")
names(x)



x<-dna.obj
p<-parsimnet(x,prob=.99)

##Getting network names in parsimnet object
names(p)
## Setting network names names.
names(p)<-c("a","b","c","d","f","g")
names(p)

Returns the length of the longest DNA sequence

Description

ncol returns the number of columns present in a matrix.

Usage

## S4 method for signature 'Dna'
ncol(x)

Arguments

Value

an integer of length one.

Methods

signature(x = "Dna")

ncol returns the number of columns present in the sequence matrix (length of the longest DNA sequence).

See Also

length-methods

Examples

data("dna.obj")
x <-dna.obj

## Giving the length of the longest sequence.
ncol(x) 
# gives the same result
length(x) 

Returns the number of DNA sequences

Description

nrow returns the number of rows present in a matrix.

Usage

## S4 method for signature 'Dna'
nrow(x)

Arguments

Value

an integer of length one.

Methods

signature(x = "Dna")

nrow returns the number of rows present in the sequence matrix (number of sequences).

Examples

data("dna.obj")
x <-dna.obj

## Giving the number of sequences.
nrow(x)

Provides the pairwise PhiST between populations

Description

This function calculates pairwise PhiST between populations using the AMOVA framework.

Usage

## S4 method for signature 'Dna'
pairPhiST(x,populations,indels="sic",nperm=99, negatives=FALSE, subset =NULL, 
showprogbar=TRUE)
## S4 method for signature 'dist'
pairPhiST(x,populations,nperm=99, negatives=FALSE, subset=NULL,showprogbar=TRUE)
## S4 method for signature 'matrix'
pairPhiST(x,populations,nperm=99,negatives=FALSE, subset=NULL,showprogbar=TRUE)

Arguments

Details

The null distribution of pairwise PhiST under the hypothesis of no difference between the populations is obtained by permuting individuals between populations.

Value

a list with following components:

Methods

signature(x = "Dna")

signature(x = "dist")

signature(x = "matrix")

Note

An internal code Statphi is taken from package ade4 version 1.7-8 without any modification, author Sandrine Pavoine. Function amova from package pegas is used internally to estimate variance components, author Emmanuel Paradis.

Author(s)

Caner Aktas, caktas.aca@gmail.com

References

Excoffier, L., Smouse, P.E. and Quattro, J.M. (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479-491.

Examples

data("dna.obj")

### Method for signature 'Dna'.
x<-dna.obj
x<-dna.obj[c(1,20,21,26,27,28,30,3,4,7,13,14,15,16,23,24,25),,as.matrix=FALSE]
populations<-c("pop1","pop1","pop1","pop1","pop1","pop1","pop1","pop2",
"pop2","pop2","pop2","pop2","pop3","pop4","pop3","pop4","pop4")

##skip permutation testing
pst<-pairPhiST(x, populations, nperm=0)
pst

##allow negative PhiST values
pst<-pairPhiST(x, populations, nperm=0, negatives=TRUE)
pst

##Gaps as missing characters.
pst<-pairPhiST(x, populations, indels="m", nperm=0, negatives=TRUE)
pst

##using subset, second population against others
pst <-pairPhiST(x, populations, nperm=0,subset=c(2))
pst


## Not run: 
## 999 permutations.
pst<-pairPhiST(x, populations, nperm=999,showprogbar=TRUE)
pst

## random populations
x<-dna.obj
populations<-sample(1:4,nrow(x),replace=TRUE)
pst<-pairPhiST(x, populations, nperm=999,showprogbar=TRUE)
pst

## populations based on clusters
x<-dna.obj
d<-distance(x)
hc<-hclust(d,method="ward.D")
populations<-cutree(hc,4)
pst<-pairPhiST(x, populations, nperm=999,showprogbar=TRUE)
pst

## End(Not run)

### Method for signature 'dist'.
x<-dna.obj
x<-dna.obj[c(1,20,21,26,27,28,30,3,4,7,13,14,15,16,23,24,25),,as.matrix=FALSE]
populations<-c("pop1","pop1","pop1","pop1","pop1","pop1","pop1","pop2",
"pop2","pop2","pop2","pop2","pop3","pop4","pop3","pop4","pop4")
d<-distance(x)
pst<-pairPhiST(d, populations, nperm=0)
pst

### Method for signature 'matrix'.
x<-dna.obj
x<-dna.obj[c(1,20,21,26,27,28,30,3,4,7,13,14,15,16,23,24,25),,as.matrix=FALSE]
populations<-c("pop1","pop1","pop1","pop1","pop1","pop1","pop1","pop2",
"pop2","pop2","pop2","pop2","pop3","pop4","pop3","pop4","pop4")
d<-as.matrix(distance(x))
pst<-pairPhiST(d, populations, nperm=0)
pst

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

Description

Function provides pairwise Nei's raw number of nucleotide differences between populations.

Usage

## S4 method for signature 'Dna'
pairnei(x,populations,indels="sic",nperm=99, subset=NULL,showprogbar=FALSE)
## S4 method for signature 'dist'
pairnei(x,populations,nperm=99, subset=NULL,showprogbar=FALSE)
## S4 method for signature 'matrix'
pairnei(x,populations,nperm=99, subset=NULL,showprogbar=FALSE)

Arguments

Details

The null distribution of pairwise Nei's differences under the hypothesis of no difference between the populations is obtained by permuting individuals between populations.

Value

a list with following components:

Methods

signature(x = "Dna")

signature(x = "dist")

signature(x = "matrix")

Author(s)

Caner Aktas, caktas.aca@gmail.com

References

Nei, M. and Li, W. H. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the United States of America 76, 5269-5273.

Examples

data("dna.obj")


### Method for signature 'Dna'.
x<-dna.obj
x<-dna.obj[c(1,20,21,26,27,28,30,3,4,7,13,14,15,16,23,24,25),,as.matrix=FALSE]
populations<-c("pop1","pop1","pop1","pop1","pop1","pop1","pop1","pop2",
"pop2","pop2","pop2","pop2","pop3","pop4","pop3","pop4","pop4")

##skip permutation testing
pn<-pairnei(x, populations, nperm=0)
pn

#Between populations
as.dist(pn$neidist)

#Within populations
diag(pn$neidist)

##Gaps as missing characters.
pn <-pairnei(x, populations, indels="m", nperm=0)
pn

##using subset, third population against others
pn<-pairnei(x, populations, nperm=0,subset=c(3))
pn

## Not run: 
## 999 permutations.
pn<-pairnei(x, populations, nperm=999, showprogbar=TRUE)
pn

## random populations
x<-dna.obj
populations<-sample(1:4,nrow(x),replace=TRUE)
pn<-pairnei(x, populations, nperm=999, showprogbar=TRUE)
pn

## populations based on clusters
x<-dna.obj
d<-distance(x)
hc<-hclust(d,method="ward.D")
populations<-cutree(hc,4)
pn<-pairnei(x, populations, nperm=999, showprogbar=TRUE)
pn

## End(Not run)

### Method for signature 'dist'.
x<-dna.obj
x<-dna.obj[c(1,20,21,26,27,28,30,3,4,7,13,14,15,16,23,24,25),,as.matrix=FALSE]
populations<-c("pop1","pop1","pop1","pop1","pop1","pop1","pop1","pop2",
"pop2","pop2","pop2","pop2","pop3","pop4","pop3","pop4","pop4")
d<-distance(x)
pn<-pairnei(d, populations,nperm=0)
pn

### Method for signature 'matrix'.
x<-dna.obj
x<-dna.obj[c(1,20,21,26,27,28,30,3,4,7,13,14,15,16,23,24,25),,as.matrix=FALSE]
populations<-c("pop1","pop1","pop1","pop1","pop1","pop1","pop1","pop2",
"pop2","pop2","pop2","pop2","pop3","pop4","pop3","pop4","pop4")
d<-as.matrix(distance(x))
pn<-pairnei(d, populations,nperm=0)
pn

Estimates gene genealogies using statistical parsimony

Description

Function for estimating gene genealogies from DNA sequences or user provided absolute pairwise character difference matrix using statistical parsimony.

Usage

## S4 method for signature 'Dna'
parsimnet(x,indels="sic",prob=.95)
## S4 method for signature 'dist'
parsimnet(x,seqlength,prob=.95)
## S4 method for signature 'matrix'
parsimnet(x,seqlength,prob=.95)

Arguments

Details

The network estimation methods implemented in parsimnet function finds one of the most parsimonious network (or sub-networks if connection between haplotypes exceeds the parsimony limit). This is an implemetation of the TCS method proposed in Templeton et al. (1992) and Clement et al. (2002).parsimnet function generates an unambiguous haplotype network without loops. If more than one best networks found (results in ambiguous connections), only a network with the lowest average all-pairs distance is returned. Loops may occur only if they are present in initial haplotype distance matrix.

Value

S4 methods for signature 'Dna', 'matrix' or 'dist' returns an object of class Parsimnet.

Methods

signature(x = "Dna")

estimating gene genealogies from DNA sequences.

signature(x = "dist")

estimating gene genealogies from distance matrix (dist object).

signature(x = "matrix")

estimating gene genealogies from distance matrix.

Note

Duplicate names in the final distance matrices in slot d are renamed without warning. An internal function .TempletonProb is taken from package pegas version 0.6 without any modification, authors Emmanuel Paradis, Klaus Schliep.

Author(s)

Caner Aktas, caktas.aca@gmail.com.

References

Clement, M., Q. Snell, P. Walker, D. Posada, and K. A. Crandall (2002) TCS: Estimating Gene Genealogies in First IEEE International Workshop on High Performance Computational Biology (HiCOMB)

Templeton, A. R., Crandall, K. A. and Sing, C. F. (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics, 132, 619-635.

See Also

network, plot-methods and pieplot-methods

Examples

	
## Not run: 
data("dna.obj")
x<-dna.obj

### Method for signature 'Dna'.
## statistical parsimony with 95
p<-parsimnet(x) 
p
plot(p)

## statistical parsimony with 99
p<-parsimnet(x,prob=.99) 
p
# plot the first network
plot(p,net=1) 

## statistical parsimony with 99
#indels are coded as missing
p<-parsimnet(x,indels="m",prob=.99)
p
plot(p)


# statistical parsimony without connection limit.
p<-parsimnet(x,prob=NULL) 
p
plot(p)


# plot the first network
plot(p,net=1)

### Method for signature 'dist'.
d<-distance(x)
seqlength<-length(x)
## statistical parsimony with 95
p<-parsimnet(d,seqlength) 
p
plot(p)

### Method for signature 'matrix'.
d<-as.matrix(distance(x))
seqlength<-length(x)
## statistical parsimony with 95
p<-parsimnet(d,seqlength)
p
plot(p)


## End(Not run)

Add Legends to Plots

Description

This function can be used to add legends to pie charts produced using pieplot.

Usage

## S4 method for signature 'Parsimnet,Haplotype'
pielegend(p,h,net=1,factors,...)

Arguments

Details

This method calls legend {graphics}, some default parameters changed:

col

an integer or character vector for the edge colors. By default, it is rainbow.

fill

an integer or character vector for the filling colors. By default, it is rainbow

legend

a numeric or character vector to appear in the legend. By default, it is the levels of the grouping factor for haplotypes.

x

position of the legend. Default is set to "topright".

Value

See ‘ legend {graphics}’

Methods

signature(p = "Parsimnet", h = "Haplotype")

Author(s)

Caner Aktas, caktas.aca@gmail.com.

See Also

plot,Parsimnet-method,floating.pie, plot.default, plot.network.default and legend.

Examples

data("dna.obj")
x<-dna.obj
h<-haplotypes::haplotype(x)

### Statistical parsimony with 95% connection limit 
p<-parsimnet(x) 

#randomly generated populations
pop<-c("pop1","pop2","pop3","pop4","pop5","pop6","pop7","pop8")
set.seed(5)
pops<-sample(pop,nrow(x),replace=TRUE)

## Plotting with default parameters.
pieplot(p,h,1, pops)

## Add legend with default parameters.
pielegend(p,h,1,pops)

## Change colors for the populations.
#8 colors for 8 populations 
cols<-colors()[c(30,369,552,558,538,642,142,91)]
pieplot(p,h,1, pops,col=cols)
pielegend(p,h,1,pops,col= cols)

Plots pie charts on statistical parsimony network

Description

Plotting pie charts on the statistical parsimony network.

Usage

## S4 method for signature 'Parsimnet,Haplotype'
pieplot(x,y,net=1,factors, coord = NULL,inter.labels=FALSE,interactive=FALSE,rex=1,...)

Arguments

Details

This method calls floating.pie {plotrix}, network.vertex {network}, and plot.default, lines, and text {graphics}. This method also uses some internal structures of plot.network.default from package network. The following additional arguments can be passed to these functions:

mode

the vertex placement algorithm. Default is set to "fruchtermanreingold".

pad

amount to pad the plotting range; useful if labels are being clipped. Default is set to 1.

displaylabels

boolean; should vertex labels be displayed?

label

a vector of vertex labels. By default, the rownames of the distance matrix (rownames(p@d[[net]])) are used. If inter.labels==FALSE only haplotype labels are displayed.

label.cex

character expansion factor for labels. Default is set to 0.75.

label.col

an integer or character vector for the label colors. By default, it is 1 (black).

label.pos

position at which labels should be placed relative to vertices. 0 and 6 results in labels which are placed away from the center of the plotting region; 1, 2, 3, and 4 result in labels being placed below, to the left of, above, and to the right of vertices, respectively; and label.pos 5 or greater than 6 results in labels which are plotted with no offset (i.e., at the vertex positions). Default is set to 0.

label.pad

amount to pad the labels. This setting is available only if the labels are plotted with offset relative to vertex positions. Default is set to 1.

vertex.cex

a numeric vector of expansion factor for intermediate vertices (only). By default it is (0.5)*min(radius). Use 'radius' to specify size of pie charts.

col

the colors of the pie sectors (i.e., colors for populations), by default rainbow.

vertex.col

an integer or character vector for the intermediate vertex colors. By default, it is 1 (black).

edge.col

an integer or character vector for the edge colors. By default, it is 1 (black).

edge.lwd

a numeric vector, edges line width. By default, it is 1.

edge.lty

a numeric vector of length one, specifies the line type for the edges. By default it is 1.

edges

the number of lines forming a pie circle, By default, it is 200.

radius

a numeric vector of length p@nhap[net] for the radius of drawn pie charts. Useful for specifying the radius independent of the haplotype frequencies. Default is (0.8*(haplotype frequencies)*rex)/max(haplotype frequencies).

vertex.sides

number of polygon sides for vertices. Default is set to 50.

xlab

x axis label.

xlab

y axis label.

Value

A two-column matrix containing the vertex positions as x,y coordinates.

Methods

signature(x = "Parsimnet", y = "Haplotype")

Note

Some internal structures of plot.network.default is taken from package network with modifications, author Carter T. Butts.

Author(s)

Caner Aktas, caktas.aca@gmail.com.

See Also

plot,Parsimnet-method,floating.pie, plot.default and plot.network.default

Examples

data("dna.obj")
x<-dna.obj
h<-haplotypes::haplotype(x)

### Statistical parsimony with 95% connection limit 
p<-parsimnet(x) 

#randomly generated populations
pop<-c("pop1","pop2","pop3","pop4","pop5","pop6","pop7","pop8")
set.seed(5)
pops<-sample(pop,nrow(x),replace=TRUE)

## Plotting with default parameters.
pieplot(p,h,1, pops)

## Change colors for the populations.
#8 colors for 8 populations 
cols<-colors()[c(30,369,552,558,538,642,142,91)]
pieplot(p,h,1, pops,col=cols)

## Expanding pie charts and intermediate vertices.
pieplot(p,h,1, pops,rex=2)

## Adjusting intermediate vertex sizes.
pieplot(p,h,1, pops, vertex.cex=rep(0.2, nrow(p@d[[1]])-p@nhap))

## Expanding pie charts and intermediate vertices, adjusting intermediate vertex sizes.
pieplot(p,h,1, pops,rex=2, vertex.cex=rep(0.1, nrow(p@d[[1]])-p@nhap))

## Adjusting radius of pie charts.
pieplot(p,h,1, pops,radius=rep(1, p@nhap))

## Not run:  
## Interactively adjusting vertex positions.
pieplot(p,h,1, pops, interactive=TRUE)

## End(Not run)

### Multiple networks with 99% connection limit.
p<-parsimnet(x,prob=.99) 

## Plotting first network with default parameters.
pieplot(p,h,1, pops)

## Change colors for the populations.
#8 colors for 8 populations
cols<-colors()[c(30,369,552,558,538,642,142,91)]
pieplot(p,h,1, pops,col=cols)

Methods for function plot in the package haplotypes

Description

Plots statistical parsimony networks.

Usage

## S4 method for signature 'Parsimnet'
plot(x,y,net=1,inter.labels=FALSE,...)
 

Arguments

Details

These methods call plot.network.default from package network. Some default parameters are changed:

label

a vector of vertex labels. By default the row names of the distance matrices in slot d are used. If inter.labels==FALSE only haplotype labels are displayed.

usearrows

boolean; should arrows (rather than line segments) be used to indicate edges? Default is set to FALSE.

mode

the vertex placement algorithm. Default is set to "kamadakawai".

pad

amount to pad the plotting range; useful if labels are being clipped. Default is set to 1.

label.cex

character expansion factor for label text. Default is set to 0.75.

vertex.cex

a numeric vector of expansion factor for vertices. By default it is 0.8 for haplotypes and 0.5 for intermediates.

vertex.col

an integer or character vector for the vertex colors. By default it is 2 (red) for haplotypes and 4 (blue) for intermediates.

Value

A two-column matrix containing the vertex positions as x,y coordinates.

Methods

signature(x = "Parsimnet",y = "missing")

Plots Parsimnet objects.

Author(s)

Caner Aktas, caktas.aca@gmail.com.

See Also

parsimnet, plot.default and plot.network.default

Examples

	
	
## Not run: 
	
data("dna.obj")
x<-dna.obj


### Method for signature 'Parsimnet'.

## Statistical parsimony with 95
p<-parsimnet(x) 
p
## Plotting with default parameters.
plot(p)

## Displaying vertex labels of intermediate haplotypes.
plot(p, inter.labels=TRUE)

## Interactively adjusting vertex positions.
plot(p, interactive=TRUE)

## Interactively adjusting and saving vertex positions.
p<-parsimnet(x)
#saving vertex positions as x,y coordinates. 
coo<-plot(p,interactive=TRUE) 
#reuse saved coordinates.
plot(p,coord=coo)

## Adjusting vertex sizes.
plot(p, vertex.cex=c(rep(3,nrow(p@d[[1]]))))
# different sizes for haplotypes and intermediates
plot(p, vertex.cex=c(rep(3,p@nhap),rep(1,c(nrow(p@d[[1]])-p@nhap)))) 

## Adjusting vertex colors
# different color for haplotypes and intermediates
plot(p, vertex.col=c(rep("magenta",p@nhap),rep("deepskyblue3",c(nrow(p@d[[1]])-p@nhap))))  
 
## Statistical parsimony with 98
p<-parsimnet(x,prob=.99) 
p
#plot the first network
plot(p,net=1)
#plot the second network
plot(p,net=2)
#plot the third network. It is a single vertex.
plot(p,net=3) 






## End(Not run)

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

Description

This function displays the polymorphic sites (base substitutions and indels) between the two sequences.

Usage

## S4 method for signature 'Dna'
polymorp(x,pair,indels="sic")

Arguments

Value

a list with two components:

indels:

a list of matrices of the indel regions if indels=="sic". The component names of the list gives the position of the indels.

subst:

a list of matrices of the base substitutions. If indels=="5th", each gap is treated as a base substitution. The component names of the list gives the position of the base substitutions.

Methods

signature(x = "Dna")

Showing base substitutions and indels between the two sequences.

Author(s)

Caner Aktas, caktas.aca@gmail.com

See Also

indelcoder and subs

Examples

data("dna.obj")
x<-dna.obj

## Showing base substitutions and indels between seq1 and seq6.

# gaps are coded following the simple indel coding method
polymorp(x,c(1,6),indels="s")

# gaps are coded as a fifth state character
polymorp(x,c(1,6),indels="5")

# gaps are treated as missing character 
polymorp(x,c(1,6),indels="m")

Returns the minimum and maximum lengths of the DNA sequences

Description

range returns the lengths of shortest and longest DNA sequences.

Usage

## S4 method for signature 'Dna'
range(x)

Arguments

Value

an integer of length two.

Methods

signature(x = "Dna")

range

See Also

length-methods

Examples

data("dna.obj")
x <-dna.obj

## shortest and longest DNA sequence lengths
range(x) 

Read sequences from a file in FASTA format

Description

Read DNA sequences from a file in FASTA Format.

Usage

read.fas(file)

Arguments

Value

read.fas returns an object of class Dna.

Note

By default, valid characters are "A","C","G","T","a","c","g","t","-","?" for the class Dna. Numeric entries (integers) between 0-5 will be converted to "?","A","C","G","T","-", respectively. Invalid characters will be replaced with "?" with a warning message.

Author(s)

Caner Aktas, caktas.aca@gmail.com

See Also

Dna

Examples

##Reading example file.	
f<-system.file("example.fas",package="haplotypes")
 
# invalid character 'N' was replaced with '?' with a warning message
x<-read.fas(file=f) 

# an object of class 'Dna'
x

Removing gaps from Dna object

Description

Removing gaps("-") from Dna object

Usage

## S4 method for signature 'Dna'
remove.gaps(x,entire.col=FALSE)

Arguments

Details

If entire.col==TRUE, alignment is preserved. If it is FALSE, end gaps are introduced to sequence matrix.

Value

an object of class Dna.

Methods

signature(x = "Dna")

Author(s)

Caner Aktas, caktas.aca@gmail.com

Examples

data("dna.obj")

## original data
x<-dna.obj 
range(x)
x@seqlengths

## Only gaps '-' are removed from sequences.
x<-remove.gaps(dna.obj, entire.col=FALSE)
range(x)
x@seqlengths

## entire columns with gaps are removed.
x<-remove.gaps(dna.obj, entire.col=TRUE)
range(x)
x@seqlengths

Retrieve or set the row names

Description

Function to get or set row names of a sequence matrix in a Dna object or distance matrix (or matrices) in a Parsimnet object.

Usage

## S4 method for signature 'Dna'
rownames(x)
## S4 method for signature 'Parsimnet'
rownames(x)
## S4 replacement method for signature 'Dna'
rownames(x)<-value
## S4 replacement method for signature 'Parsimnet'
rownames(x)<-value

Arguments

Methods

signature(x = "Dna")

signature(x = "Parsimnet")

Examples

data("dna.obj")
x<-dna.obj

### Method for signature 'Dna'.

## Getting sequence names.
rownames(x)

## Setting sequence names.
rownames(x)<-c(1:nrow(x))
rownames(x)

### Method for signature 'Parsimnet'.
x<-dna.obj

##single network
p<-parsimnet(x)

##Getting vertex names
rownames(p)

## Setting vertex names.
rownames(p)<-list(c(1:nrow(p@d[[1]])))
rownames(p)
plot(p)

## Multiple networks with 99% connection limit.
p<-parsimnet(x,prob=.99) 

## Getting vertex names
rownames(p)

## Setting vertex names.
rownames(p)<-list(1:9, 10, 11,12:13,14,15:16)
rownames(p)

Methods for function show in the package haplotypes

Description

Show objects of classes Dna, Haplotype, and Parsimnet

Methods

signature(object = "Dna")

displays Dna object briefly: The total number of DNA sequences, names of the first six sequences (if nrow(x)>=6), length of the shortest and longest sequences and the names of the slots.

signature(object = "Haplotype")

displays Haplotype object briefly: The list of individuals that share the same haplotypes, the total number of haplotypes and the names of the slots.

signature(object = "Parsimnet")

displays Parsimnet object briefly: The total number of networks, the maximum connection steps at chosen probability, the total number of haplotypes in each network,the total number of intermediates in each network, total network lengths (scores) of each network and the names of the slots.

Displays base substitutions

Description

This function displays all base substitutions. If fifth=="TRUE", each gap is treated as a fifth state character.

Usage

## S4 method for signature 'Dna'
subs(x,fifth=FALSE)

Arguments

Value

a list with three components:

subsmat:

a sequence matrix showing substitutions.

subs:

a list of matrices of the substitutions.

subsmnum:

total number of substitutions.

Methods

signature(x = "Dna")

Author(s)

Caner Aktas, caktas.aca@gmail.com.

Examples

data("dna.obj")
x<-dna.obj

## Base substitutions.
subs(x)

## Gaps are treated as a fifth state character.
subs(x,fifth=TRUE)

Convert sequence characters from upper to lower case or vice versa

Description

Convert sequence characters in a Dna object from upper to lower case or vice versa.

Usage

## S4 method for signature 'Dna'
tolower(x)
## S4 method for signature 'Dna'
toupper(x)

Arguments

Value

an object of class Dna.

Methods

signature(x = "Dna")

Examples

	
## Coercing a list to a 'Dna' object.
seq1<-c("?","A","C","g","t","-","0","1")
seq2<-c("?","A","C","g","t","-","0","1","2")
seq3<-c("?","A","C","g","t","-","0","1","2","3")
x<-list(seq1=seq1,seq2=seq2,seq3=seq3) 
dna.obj<-as.dna(x)

#characters in Dna object
table(as.matrix(dna.obj))

##all lower case
lowc<-tolower(dna.obj)
#characters
table(as.matrix(lowc))

##all upper case
upc<-toupper(dna.obj)
#characters
table(as.matrix(upc))

Extract Unique Sequences

Description

unique returns a list with duplicate sequences removed.

Usage

## S4 method for signature 'Dna'
unique(x,gaps=FALSE)

Arguments

Details

This function behaves somehow similar to haplotype, however indels and missing characters are not taken into account.

Methods

signature(x = "Dna")

Examples

	
data("dna.obj")
x<-dna.obj[1:6,,as.matrix=FALSE]

##gaps removed.
unique(x)

##gaps not removed.
unique(x,gaps=TRUE)

##unique vs. haplotype
#unique returns 5 unique sequences.
unique(x)
length(unique(x))

#haplotype returns 4 unique haplotypes with simple indel coding.
h<-haplotype(x)
as.list(as.dna(h))
length(h)

#haplotype returns 3 unique haplotypes with gaps as missing.
h<-haplotype(x, indels="m")
as.list(as.dna(h))
length(h)