TriplexViews-class: The TriplexViews class

In triplex: Search and visualize intramolecular triplex-forming sequences in DNA

Description

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.

Details

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.

Constructor

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.

Accessor-like methods

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.

Note

The only standard way to create a TriplexViews object is to use triplex.search function.

Author(s)

Jiri Hon

See Also

triplex.search, triplex.diagram, triplex.3D, XStringViews, triplex.alignment

Examples

  
seq <- DNAString("GAAGAAGAAGAAGAAGAAGAAGAAGAAGAA")
t <- triplex.search(seq, min_score=10, p_value=1)
start(t)
end(t)
score(t)
pvalue(t)
ins(t)
type(t)

# Search triplex with maximal score
t[score(t) == max(score(t))]

# Sort triplexes by score
t[order(score(t), decreasing=TRUE)]

triplex documentation built on Nov. 8, 2020, 5:34 p.m.