tables {ShortRead} | R Documentation

## Summarize XStringSet read frequencies

### Description

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

### Usage

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

### Arguments

`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

### Details

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`.

### Value

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.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### Examples

    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)

[Package ShortRead version 1.46.0 Index]