Description Details Constructor Accessor-like methods Note Author(s) See Also Examples
The TriplexViews class is a container for storing a set of triplexes
identified in the same DNA sequence (an DNAString
object).
Each triplex is defined by its start/end locations, score, P-value,
insertion number, type, loop start, loop end and strand identification.
TriplexViews object contains also a parameter vector plus score and group tables
that stores custom algorithm options that were used for triplex search.
This is necessary for proper triplex visualization by triplex.diagram
and triplex.3D
functions.
A TriplexViews object is in fact a particular case of an
XStringViews
object (the TriplexViews class contains the
XStringViews class) so it
can be manipulated in a similar manner. See
?XStringViews
for
detailed information.
If you are interested in algorithm options that are stored in
the TriplexViews object, see parameters of triplex.search
function. These options are required by visualization functions for
proper computation of triplex alignment.
There is no public constructor for TriplexViews object as it stores search algorithm options. TriplexViews object would not be useful without algorithm options attached. For more information see description or details.
All the accessor-like methods defined for XStringViews objects work on TriplexViews objects. In addition, the following accessors are defined for TriplexViews objects:
score(x)
:
A vector of non-negative integers containing the scores of triplexes.
pvalue(x)
:
A vector of non-negative doubles containing the P-values of triplexes.
ins(x)
:
A vector of non-negative integers containing the number of insertions/deletions
in triplexes.
type(x)
:
A vector of non-negative integers containing the triplex type.
lstart(x)
:
A vector of non-negative integers containing the triplex loop starts.
lwidth(x)
:
A vector of non-negative integers containing the triplex loop widths.
lend(x)
:
A vector of non-negative integers containing the triplex loop ends.
strand(x)
:
A vector of '+' or '-' signs to identify on which strand the triplex was found.
toString(x)
:
Converts TriplexViews
object into vector of strings.
The only standard way to create a TriplexViews object
is to use triplex.search
function.
Jiri Hon
triplex.search
,
triplex.diagram
,
triplex.3D
,
XStringViews
,
triplex.alignment
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.