DNAbin

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Manipulate DNA Sequences in Bit-Level Format

These functions help to manipulate DNA sequences coded in the bit-level coding scheme.

Keywords
manip
Usage
## S3 method for class 'DNAbin':
print(x, printlen = 6, digits = 3, \dots)
## S3 method for class 'DNAbin':
rbind(\dots)
## S3 method for class 'DNAbin':
cbind(\dots, check.names = TRUE, fill.with.gaps = FALSE,
             quiet = FALSE)
## S3 method for class 'DNAbin':
[(x, i, j, drop = FALSE)
## S3 method for class 'DNAbin':
as.matrix(x, \dots)
## S3 method for class 'DNAbin':
c(\dots, recursive = FALSE)
## S3 method for class 'DNAbin':
as.list(x, \dots)
## S3 method for class 'DNAbin':
labels(object, \dots)
Details

These are all `methods' of generic functions which are here applied to DNA sequences stored as objects of class "DNAbin". They are used in the same way than the standard Rfunctions to manipulate vectors, matrices, and lists. Additionally, the operators [[ and $ may be used to extract a vector from a list. Note that the default of drop is not the same than the generic operator: this is to avoid dropping rownames when selecting a single sequence.

These functions are provided to manipulate easily DNA sequences coded with the bit-level coding scheme. The latter allows much faster comparisons of sequences, as well as storing them in less memory compared to the format used before ape 1.10.

For cbind, the default behaviour is to keep only individuals (as indicated by the rownames) for which there are no missing data. If fill.with.gaps = TRUE, a `complete' matrix is returned, enventually with insertion gaps as missing data. If check.names = TRUE (the default), the rownames of each matrix are checked, and the rows are reordered if necessary. If check.names = FALSE, the matrices must all have the same number of rows, and are simply binded; the rownames of the first matrix are used. See the examples.

as.matrix may be used to convert DNA sequences (of the same length) stored in a list into a matrix while keeping the names and the class. as.list does the reverse operation.

Value

an object of class "DNAbin" in the case of rbind, cbind, and [.

References

Paradis, E. (2007) A Bit-Level Coding Scheme for Nucleotides. http://ape.mpl.ird.fr/misc/BitLevelCodingScheme_20April2007.pdf

Paradis, E. (2012) Analysis of Phylogenetics and Evolution with R (Second Edition). New York: Springer.

See Also

as.DNAbin, read.dna, read.GenBank, write.dna, image.DNAbin

The corresponding generic functions are documented in the package base.

Aliases
Examples
data(woodmouse)
woodmouse
print(woodmouse, 15, 6)
print(woodmouse[1:5, 1:300], 15, 6)
### Just to show how distances could be influenced by sampling:
dist.dna(woodmouse[1:2, ])
dist.dna(woodmouse[1:3, ])
### cbind and its options:
x <- woodmouse[1:2, 1:5]
y <- woodmouse[2:4, 6:10]
as.character(cbind(x, y)) # gives warning
as.character(cbind(x, y, fill.with.gaps = TRUE))
as.character(cbind(x, y, check.names = FALSE)) # gives an error
Documentation reproduced from package ape, version 3.0-2, License: GPL (>= 2)

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