## Constructors:
RNAVector(x = character())
AAVector(x = character())
## Accessor-like methods: see below
"["(x, i)
"as.character"(x, use.names = TRUE)TRUE the names are
preservedDNAVector, RNAVector, AAVector return a
sequence set of identical class name
x is a
BioVector. length(x): the number of
sequences in x. width(x): vector
of integer values with the number of bases/amino acids
for each sequence in the set. names(x):
character vector of sample names. x is a
BioVector. x[i]: return a BioVector
object that only contains the samples selected with the
subsetting parameter i. This parameter can be a
numeric vector with indices or a character vector which
is matched against the names of x. Element related
metadata is subsetted accordingly if available. c(x, ...): return a sequence set that is a
concatination of the given sequence sets. x is a
BioVector. as.character(x,
use.names=TRUE): return the sequence set as named or
unnamed character vector dependent on the use.names
parameter. DNAVector is used for storing DNA
sequences, RNAVector for RNA sequences and
AAVector for amino acid sequences. The class
BioVector is derived from the R base type
character representing a vector of character
strings. It is an abstract class which can not be
instantiated. BioVector is the parent class for
DNAVector, RNAVector and AAVector. For
the three derived classes identically named functions exist
which are constructors. It should be noted that the
constructors only wrap the sequence data into a class
without copying or recoding the data. The functions
provided for DNAVector, RNAVector and
AAVector classes are only a very small subset
compared to those of XStringSet but are
designed along their counterparts from the Biostrings
package. Assignment of metadata and element
metadata via mcols is supported for the
DNAVector, RNAVector and AAVector
objects similar to objects of XStringSet
derived classes (for details on metadata assignment see
annotationMetadata and
positionMetadata). In contrast to
XStringSet the BioVector derived
classes also support the storage of lowercase characters.
This can be relevant for repeat regions which are often
coded in lowercase characters. During the creation of
XStringSet derived classes the lowercase
characters are converted to uppercase automatically and the
information about repeat regions is lost. For
BioVector derived classes the user can specify
during creation of a sequence kernel object whether
lowercase characters should be included as uppercase
characters or whether repeat regions should be ignored
during sequence analysis. In this way it is possible to
perform both types of analysis on the same set of sequences
through defining one kernel object which accepts lowercase
characters and another one which ignores them.
metadata, elementMetadata,
XStringSet, DNAStringSet,
RNAStringSet, AAStringSet
## in general DNAStringSet should be prefered as described above
## create DNAStringSet object for a set of sequences
x <- DNAStringSet(c("AACCGCGATTATCGatatatatatatatatTGGAAGCTAGGACTA",
"GACTTACCCgagagagagagagaCATGAGAGGGAAGCTAGTA"))
## assign names to the sequences
names(x) <- c("Sample1", "Sample2")
## to show the different handling of lowercase characters
## create DNAVector object for the same set of sequences and assign names
xv <- DNAVector(c("AACCGCGATTATCGatatatatatatatatTGGAAGCTAGGACTA",
"GACTTACCCgagagagagagagaCATGAGAGGGAAGCTAGTA"))
names(xv) <- c("Sample1", "Sample2")
## show DNAStringSet object - lowercase characters were translated
x
## in the DNAVector object lowercase characters are unmodified
## their handling can be defined at the level of the sequence kernel
xv
## show number of the sequences in the set and their number of characters
length(xv)
width(xv)
nchar(xv)
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