ShortRead-class {ShortRead} | R Documentation |
This class provides a way to store and manipulate, in a coordinated fashion, uniform-length short reads and their identifiers.
Objects from this class are not normally created directly by the user.
sread
:"DNAStringSet"
containing IUPAC-standard, uniform-length DNA strings represent
short sequence reads.id
:"BStringSet"
containing
identifiers, one for each short read.
Class ".ShortReadBase"
, directly.
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.signature(x = "ShortRead")
: returns a
integer(1)
vector describing the number of reads in this
object.signature(x = "ShortRead")
: returns a
integer(1)
vector describing the number of characters in
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(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(object = "ShortRead")
: provides a
more extensive summary of this object, displaying the first and
last entries of sread
and id
.Martin Morgan
showClass("ShortRead") showMethods(class="ShortRead")