plotDomainogramNearViewpoint: Plot domainogram of interaction regions near the viewpoint

In r3Cseq: Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)

Description

Plot domainogram of interaction regions near the viewpoint

Usage

plotDomainogramNearViewpoint(object,smoothing.parameter=0.1,distance=5e5,maximum_window=25e3,view=c("experiment","control","both"))

Arguments

object	r3Cseq or r3CseqInBatch object
smoothing.parameter	A level at which cubic smoothing spline for the spar (see vsmooth.spline) input parameter. Must be in (0.06,0.4] (default=0.1)
distance	Numeric. The distance relative to the viewpoint (default=5e5)
maximum_window	Numeric. The maximum windowing (default=25e3). We normally compute the interaction regions per window starting from 2Kb to maximum window (default=25kb) to make the interaction matrix for visualizing the domainogram.
view	character. The selected view of data (default="experiment")

Value

Plots of domainogram for interaction regions close to the viewpoint

Author(s)

S. Thongjuea

See Also

plotOverviewInteractions, plotInteractionsPerChromosome, plotInteractionsNearViewpoint

Examples

	# See the vignette

r3Cseq documentation built on Nov. 8, 2020, 6:26 p.m.