Description Usage Arguments Details Value Author(s) Examples

This generic summarizes the number of times each sequence occurs in an
`XStringSet`

instance.

1 |

`x` |
An object for which a |

`n` |
An |

`...` |
Additional arguments available to methods |

Methods of this generic summarize the frequency with which each read occurs, There are two components to the summary. The reads are reported from most common to least common; typically a method parameter controls how many reads to report. Methods also return a pair of vectors describing how many reads were represented 1, 2, ... times.

The following methods are defined, in addition to methods described in class-specific documentation:

- tables
`signature(x= "XStringSet", n = 50)`

: Apply`tables`

to the`XStringSet`

`x`

.

A list of length two.

`top` |
A named integer vector. Names correspond to sequences.
Values are the number of times the corresponding sequence occurs in
the |

`distribution` |
a |

Martin Morgan <[email protected]>

1 2 3 4 5 6 | ```
showMethods("tables")
sp <- SolexaPath(system.file("extdata", package="ShortRead"))
aln <- readAligned(sp)
tables(sread(aln), n=6)
lattice::xyplot(log10(nReads)~log10(nOccurrences),
tables(sread(aln))$distribution)
``` |

ShortRead documentation built on May 2, 2018, 2:12 a.m.

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