Dna-class: Class '"Dna"' in the Package 'haplotypes'

In haplotypes: Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony

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, [e-mail]

haplotypes documentation built on July 26, 2023, 5:22 p.m.