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 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.

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.
append
signature(x = "ShortRead", values = "ShortRead", length = "missing"): 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. A user-supplied argument ranges is ignored by this method; the class of the return object is the same as the class of 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(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 1.2.1 Index]