ShortRead-class {ShortRead}R Documentation

"ShortRead" class for short reads

Description

This class provides a way to store and manipulate, in a coordinated fashion, uniform-length short reads and their identifiers.

Objects from the Class

Objects from this class are not normally created directly by the user.

Slots

sread:
Object of class "DNAStringSet" containing IUPAC-standard, uniform-length DNA strings represent short sequence reads.
id:
Object of class "BStringSet" containing identifiers, one for each short read.

Extends

Class ".ShortReadBase", directly.

Methods

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.
length
signature(x = "ShortRead"): returns a integer(1) vector describing the number of reads in this object.
width
signature(x = "ShortRead"): returns a integer(1) vector describing the number of characters in each read in this object.
srorder
\signature{x = "ShortRead"}:
srrank
\signature{x = "ShortRead"}:
srsort
\signature{x = "ShortRead"}:
srduplicated
\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.
srdistance
\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.
alphabetByCycle
signature(stringSet = "ShortRead"): Apply alphabetByCycle to the sread component of stringSet, returning a matrix as described in alphabetByCycle.
tables
signature(x= "ShortRead", n = 50): Apply tables to the sread component of x, returning a list summarizing frequency of reads in x.
clean
signature(object="ShortRead"): Remove all reads containing non-nucleotide ("N", "-") symbols.
show
signature(object = "ShortRead"): provides a brief summary of the object, including its class, length and width.
detail
signature(object = "ShortRead"): provides a more extensive summary of this object, displaying the first and last entries of sread and id.

Author(s)

Martin Morgan

See Also

ShortReadQ

Examples

showClass("ShortRead")
showMethods(class="ShortRead")

[Package ShortRead version 1.0.7 Index]