ShortRead-class: "ShortRead" class for short reads

In ShortRead: FASTQ input and manipulation

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.

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.

Author(s)

Martin Morgan

See Also

ShortReadQ

Examples

showClass("ShortRead")
showMethods(class="ShortRead", where=getNamespace("ShortRead"))

ShortRead documentation built on Nov. 8, 2020, 8:02 p.m.