## S3 method for class 'DNAbin':
print(x, \dots)
## S3 method for class 'DNAbin':
summary(object, printlen = 6, digits = 3, \dots)
## S3 method for class 'DNAbin':
rbind(\dots)
## S3 method for class 'DNAbin':
cbind(\dots, check.names = TRUE)
## S3 method for class 'DNAbin':
[(x, i, j, drop = TRUE)
## S3 method for class 'DNAbin':
as.matrix(x, \dots)
"DNAbin"
.print
, summary
, and
as.matrix
, or a series of objects of class "DNAbin"
in
the case of rbind
and TRUE
(the default), the returned object
is of the lowest possible dimension."DNAbin"
in the case of rbind
,
cbind
, and [
."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
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.
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.DNAbin
, read.dna
,
read.GenBank
, write.dna
The corresponding generic functions are documented in the package
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, ])
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