triplex (version 1.12.0)

triplex.3D: Triplex visualization, 3D representation

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.

Value

Instance of DNAStringSet object with computed alignment.

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

triplex3d.png

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)