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These functions help to manipulate DNA sequences coded in the bit-level coding scheme.
# S3 method for DNAbin
print(x, printlen = 6, digits = 3, ...)
# S3 method for DNAbin
rbind(...)
# S3 method for DNAbin
cbind(..., check.names = TRUE, fill.with.gaps = FALSE,
quiet = FALSE)
# S3 method for DNAbin
[(x, i, j, drop = FALSE)
# S3 method for DNAbin
as.matrix(x, ...)
# S3 method for DNAbin
c(..., recursive = FALSE)
# S3 method for DNAbin
as.list(x, ...)
# S3 method for DNAbin
labels(object, ...)an object of class "DNAbin" in the case of rbind,
cbind, and [.
an object of class "DNAbin".
either further arguments to be passed to or from other
methods in the case of print, as.matrix, and
labels, or a series of objects of class "DNAbin" in the
case of rbind, cbind, and c.
the number of labels to print (6 by default).
the number of digits to print (3 by default).
a logical specifying whether to check the rownames before binding the columns (see details).
a logical indicating whether to keep all
possible individuals as indicating by the rownames, and eventually
filling the missing data with insertion gaps (ignored if
check.names = FALSE).
a logical to switch off warning messages when some rows are dropped.
indices of the rows and/or columns to select or to drop. They may be numeric, logical, or character (in the same way than for standard R objects).
logical; if TRUE, the returned object is of the
lowest possible dimension.
for compatibility with the generic (unused).
Emmanuel Paradis
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 R functions 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 some rownames are duplicated,
an error is returned). 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.
Paradis, E. (2007) A Bit-Level Coding Scheme for Nucleotides. https://emmanuelparadis.github.io/misc/BitLevelCodingScheme_20April2007.pdf
Paradis, E. (2012) Analysis of Phylogenetics and Evolution with R (Second Edition). New York: Springer.
as.DNAbin, read.dna,
read.GenBank, write.dna,
image.DNAbin,AAbin
The corresponding generic functions are documented in the package base.
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))
if (FALSE) {
as.character(cbind(x, y, check.names = FALSE)) # gives an error
}
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