tables {ShortRead} | R Documentation |
This generic summarizes the number of times each sequence occurs in an
XStringSet
instance.
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:
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) xyplot(log10(nReads)~log10(nOccurrences), tables(sread(aln))$distribution)