Description Usage Arguments Details Value Author(s) Examples

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`

.

1 2 3 4 |

`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:

- srsort
`signature(x = "XStringSet")`

:- srorder
`signature(x = "XStringSet")`

:- srduplicated
`signature(x = "XStringSet")`

:Apply

`srorder`

,`srrank`

,`srsort`

,`srduplicated`

to`XStringSet`

objects such as those returned by`sread`

.- srsort
`signature(x = "ShortRead")`

:- srorder
`signature(x = "ShortRead")`

:- srduplicated
`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>

1 2 3 4 5 6 7 8 9 10 | ```
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))
``` |

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