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

Description

S4 class to hold DNA sequence data.

Arguments

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".
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.
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.
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 Nei's average number of differences 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.
show: signature(object = "Dna"): displays Dna object briefly.
subs: signature(x = "Dna"): displays information about base substitutions.