| ShortRead-class {ShortRead} | R Documentation |
This class provides a way to store and manipulate, in a coordinated fashion, uniform-length short reads and their identifiers.
Objects from this class are not normally created directly by the user.
sread:"DNAStringSet"
containing IUPAC-standard, uniform-length DNA strings represent
short sequence reads.id:"BStringSet" containing
identifiers, one for each short read.
Class ".ShortReadBase", directly.
See accessors for slot accessor functions.
signature(x = "ShortRead", i = "ANY", j = "missing"):
This method creates a new ShortRead object containing only
those reads indexed by i. Additional methods on
‘[,ShortRead’ do not provide additional functionality, but
are present to limit inappropriate use.signature(x = "ShortRead"): returns a
integer(1) vector describing the number of reads in this
object.signature(x = "ShortRead"): returns a
integer(1) vector describing the number of characters in
each read in this object.\signature{x = "ShortRead"}:\signature{x = "ShortRead"}:\signature{x = "ShortRead"}:\signature{x = "ShortRead"}:
Order, rank, sort, and find duplicates in ShortRead objects
based on sread(x), analogous to the corresponding functions
order, rank, sort, and duplicated,
ordering nucleotides in the order ACGT.\signature{pattern="ShortRead", subject="ANY"}:
Find the edit distance between each read in pattern and the
(short) sequences in subject. See srdistance
for allowable values for subject, and for additional
details.signature(stringSet = "ShortRead"):
Apply alphabetByCycle to the sread component
of stringSet, returning a matrix as described in
alphabetByCycle.signature(x= "ShortRead", n = 50):
Apply tables to the sread component of
x, returning a list summarizing frequency of reads in
x.signature(object="ShortRead"): Remove all reads
containing non-nucleotide ("N", "-") symbols.signature(object = "ShortRead"): provides a brief
summary of the object, including its class, length and width.signature(object = "ShortRead"): provides a
more extensive summary of this object, displaying the first and
last entries of sread and id.Martin Morgan
showClass("ShortRead")
showMethods(class="ShortRead")