DNAbin {ape} | R Documentation |
These functions help to manipulate DNA sequences coded in the bit-level coding scheme.
## S3 method for class 'DNAbin': print(x, ...) ## S3 method for class 'DNAbin': summary(object, printlen = 6, digits = 3, ...) ## S3 method for class 'DNAbin': rbind(...) ## S3 method for class 'DNAbin': cbind(..., check.names = TRUE) x[i, j, drop = TRUE]
x, object |
an object of class "DNAbin" . |
... |
either further arguments to be passed to or from other
methods in the case of print and summary , or a series
of objects of class "DNAbin" in the case of rbind and
cbind . |
printlen |
the number of labels to print (6 by default). |
digits |
the number of digits to print (3 by default). |
check.names |
a logical specifying whether to check the rownames before binding the columns (see details). |
i, j |
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). |
drop |
logical; if TRUE (the default), the returned object
is of the lowest possible dimension. |
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.
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
, if "check.names = TRUE"
, the rownames of each
matrix are checked, and the rows are reordered if necessary. If the
rownames differ among matrices, an error occurs. If
"check.names = FALSE"
, the matrices are simply binded and the
rownames of the first matrix are used.
an object of class "DNAbin"
in the case of rbind
,
cbind
, and [
.
Emmanuel Paradis Emmanuel.Paradis@mpl.ird.fr
Paradis E. 2007. A Bit-Level Coding Scheme for Nucleotides. http://pbil.univ-lyon1.fr/R/ape/misc/BitLevelCodingScheme_20April2007.pdf
as.DNAbin
, read.dna
,
read.GenBank
, write.dna
The corresponding generic functions are documented in the package base.
data(woodmouse) woodmouse summary(woodmouse) summary(woodmouse, 15, 6) summary(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, ])