This class provides a way to store and manipulate, in a coordinated fashion, uniform-length short reads and their identifiers.
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.".ShortReadBase", directly.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.signature(object = "AlignedRead"): access the
sread slot of object.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.signature(x = "ShortRead", values = "ShortRead"):
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. 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'.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(x = "ShortRead"): provides a
more extensive summary of this object, displaying the first and
last entries of sread and id.signature(object, file, ...): write
object to file in fasta format. See
writeXStringSet for ... argument values.ShortReadQ
showClass("ShortRead")
showMethods(class="ShortRead", where=getNamespace("ShortRead"))
Run the code above in your browser using DataLab