Order, sort, and find duplicates in XStringSet objects
These generics order, rank, sort, and find duplicates in short read
objects, including fastq-encoded qualities. srorder,
srrank and srsort differ from the default functions
rank, order and sort in that sorting is based on
an internally-defined order rather than, e.g., the order implied by
LC_COLLATE.
srorder(x, ...) srrank(x, ...) srsort(x, ...) srduplicated(x, ...)
x |
The object to be sorted, ranked, ordered, or to have duplicates identified; see the examples below for objects for which methods are defined. |
... |
Additional arguments available for use by methods; usually ignored. |
Unlike sort and friends, the implementation does not preserve
order of duplicated elements. Like duplicated, one element in
each set of duplicates is marked as FALSE.
srrank settles ties using the “min” criterion described
in rank, i.e., identical elements are ranked equal to the
rank of the first occurrence of the sorted element.
The following methods are defined, in addition to methods described in class-specific documentation:
signature(x = "XStringSet"):
signature(x = "XStringSet"):
signature(x = "XStringSet"):
Apply srorder, srrank, srsort,
srduplicated to
XStringSet objects such
as those returned by sread.
signature(x = "ShortRead"):
signature(x = "ShortRead"):
signature(x = "ShortRead"):
Apply srorder, srrank, srsort,
srduplicated to
XStringSet objects to
the sread component of ShortRead and
derived objects.
The functions return the following values:
srorder |
An integer vector the same length as |
srrank |
An integer vector the same length as |
srsort |
An instance of |
srduplicated |
A logical vector the same length as |
Martin Morgan <mtmorgan@fhcrc.org>
showMethods("srsort")
showMethods("srorder")
showMethods("srduplicated")
sp <- SolexaPath(system.file('extdata', package='ShortRead'))
rfq <- readFastq(analysisPath(sp), pattern="s_1_sequence.txt")
sum(srduplicated(sread(rfq)))
srsort(sread(rfq))
srsort(quality(rfq))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.