triplex.3D: Triplex visualization, 3D representation

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

Description

This function visualizes a TriplexViews object as a 3D model. Its structure can be drawn with automatic optimalizations. To use this function, please install suggested rgl package from CRAN.

Usage

triplex.3D(triplex, opt = TRUE, A.col = "red", T.col = "brown", 
           G.col = "green", C.col = "blue", bbone.col = "violet", 
           bgr.col = "white", bbone.n = 20)

Arguments

triplex	TriplexViews object including only one triplex.
opt	TRUE or FALSE: TRUE - structure of triplex will be optimalized, FALSE - structure will be drawn without optimalization.
A.col	Color of Adine base.
T.col	Color of Thymin base.
G.col	Color of Guanine base.
C.col	Color of Cytosine base.
bgr.col	Color of background.
bbone.col	Color of backbone.
bbone.n	Number of sides of backbone bonds.

Details

The input TriplexViews object is required to provide additional algorithm options (see triplex.search). These are used for proper computation of triplex alignment.

An example of a graphical output corresponding to a triplex type 3 with DNA sequence "GGAAAGCAATGCCAGGCAGGG" is shown in the following figure

Value

Instance of DNAStringSet object with computed alignment.

Author(s)

Kamil Rajdl, Jiri Hon

See Also

triplex.diagram, triplex.search, triplex.alignment

Examples

seq <- DNAString("GGAAAGCAATGCCAGGCAGGG")
t <- triplex.search(seq, min_score=10, p_value=1)
## Not run: 
triplex.3D(t[1])

## End(Not run)

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