plotTVData: Summarize plotTV results

In TransView: Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

Description

plotTVData returns the ordering and clustering results as internally calculated by plotTV.

Usage

## S4 method for signature 'TVResults'
plotTVData(tvr)

Arguments

tvr	A TVResults object as returned by plotTV

Details

If k-means or manual clustering was performed, row means per cluster will be returned in a data.frame. Otherwise row means over the whole data will be returned.

Value

Returns a data.frame of the clustering results with five columns: Position, Cluster, Sample, Average_scores and Plot

Author(s)

Julius Muller [e-mail]

See Also

• TVResults-class.

Examples

exbam<-dir(system.file("extdata", package="TransView"),full=TRUE,patt="bam$")
exls<-dir(system.file("extdata", package="TransView"),full=TRUE,patt="xls$")

exden.ctrl<-parseReads(exbam[1],verbose=0)
exden.chip<-parseReads(exbam[2],verbose=0)

peaks<-macs2gr(exls,psize=500)

cluster_res<-plotTV(exden.chip,exden.ctrl,regions=peaks,cluster=5,norm_readc=FALSE,showPlot=FALSE)
summaryTV(cluster_res)
tvdata<-plotTVData(cluster_res)

TransView documentation built on Nov. 8, 2020, 5:31 p.m.