| 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 created by readFasta, or by calls
to the constructor ShortRead, as outlined below.
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.
Constructors include:
signature(sread = "DNAStringSet", id = "BStringSet"):
Create a ShortRead object from reads and their
identifiers. The length of id must match that of sread.signature(sread = "DNAStringSet", id = "missing"):
Create a ShortRead object from reads, creating empty identifiers.signature(sread = "missing", id = "missing", ...):
Create an empty ShortRead object.
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", values = "ShortRead", length = "missing"):
append the sread and id slots of values after
the corresponding fields of x.signature(x = "ShortRead", start = NA, end = NA, width = NA, use.names = TRUE):
‘narrow’ sread so that sequences are between
start and end bases, according to
narrow in the IRanges
package.
signature(x = "ShortRead"): returns a
integer(1) vector describing the number of reads in this
object.signature(x = "ShortRead"): returns an
integer() vector of the widths of 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(Lpattern = "", Rpattern = "", subject = "ShortRead", max.Lmismatch = 0, max.Rmismatch = 0, with.Lindels = FALSE, with.Rindels = FALSE, Lfixed = TRUE, Rfixed = TRUE, ranges = FALSE):
Remove left and / or right flanking patterns from
sread(subject), as described in
trimLRPatterns. Classes
derived from ShortRead (e.g., ShortReadQ,
AlignedRead) have corresponding base quality scores
trimmed, too. A user-supplied argument ranges is ignored by
this method; the class of the return object is the same as the
class of subject.
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")