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ShortRead (version 1.30.0)

ShortRead-class: "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.

Arguments

Objects from the Class

Objects from this class are created by readFasta, or by calls to the constructor ShortRead, as outlined below.

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

Constructors include:
ShortRead
signature(sread = "DNAStringSet", id = "BStringSet"): Create a ShortRead object from reads and their identifiers. The length of id must match that of sread.
ShortRead
signature(sread = "DNAStringSet", id = "missing"): Create a ShortRead object from reads, creating empty identifiers.
ShortRead
signature(sread = "missing", id = "missing"): Create an empty ShortRead object.
Methods include:
sread
signature(object = "AlignedRead"): access the sread slot of object.
id
signature(object = "AlignedRead"): access the id slot of object.
[
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.
append
signature(x = "ShortRead", values = "ShortRead"): append the sread and id slots of values after the corresponding fields of x.
narrow
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.
length
signature(x = "ShortRead"): returns a integer(1) vector describing the number of reads in this object.
width
signature(x = "ShortRead"): returns an integer() vector of the widths of 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.
trimLRPatterns
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. The class of the return object is the same as the class of subject, except when ranges=TRUE when the return value is the ranges to use to trim 'subject'.
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(x = "ShortRead"): provides a more extensive summary of this object, displaying the first and last entries of sread and id.
writeFasta
signature(object, file, ...): write object to file in fasta format. See writeXStringSet for ... argument values.

See Also

ShortReadQ

Examples

Run this code
showClass("ShortRead")
showMethods(class="ShortRead", where=getNamespace("ShortRead"))

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