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".
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.

Author

Caner Aktas, caktas.aca@gmail.com