tables: Summarize XStringSet read frequencies
In ShortRead: FASTQ input and manipulation

Description Usage Arguments Details Value Author(s) Examples

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

1	tables(x, n=50, ...)

`x`	An object for which a `tables` method is defined.
`n`	An `integer(1)` value determining how many named sequences will be present in the `top` portion of the return value.
`...`	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 `XStringSet`. The vector is sorted in decreasing order; methods typically include a parameter specifying the number of sequences to return.
`distribution`	a `data.frame` with two columns. `nOccurrences` is the number of times any particular sequence is represented in the set (1, 2, ...). `nReads` is the number of reads with the corresponding occurrence.

Martin Morgan <mtmorgan@fhcrc.org>

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)