plotFeatureBoundaryCoverage: plotFeatureBoundaryCoverage

In RCAS: RNA Centric Annotation System

Description

This function is used to create interactive plots displaying 5' and 3' end coverage profiles of given transcript features.

Usage

plotFeatureBoundaryCoverage(cvgF, cvgT, featureName)

Arguments

cvgF	data.frame object containing 'fiveprime' coverage data returned by getFeatureBoundaryCoverage function
cvgT	data.fram object containing 'threeprime' coverage data returned by getFeatureBoundaryCoverage function
featureName	character object. This is used to label the axes (e.g. transcripts, exons)

Value

a plotly htmlwidget is returned

Examples

data(queryRegions)
data(gff)
txdb <- GenomicFeatures::makeTxDbFromGRanges(gff)
transcriptCoords <- GenomicFeatures::transcripts(txdb)
cvgF <- getFeatureBoundaryCoverage (queryRegions = queryRegions,
                                    featureCoords = transcriptCoords,
                                    flankSize = 100,
                                    boundaryType = 'fiveprime',
                                    sampleN = 1000)
                                    
cvgT <- getFeatureBoundaryCoverage (queryRegions = queryRegions,
                                    featureCoords = transcriptCoords,
                                    flankSize = 100,
                                    boundaryType = 'threeprime',
                                    sampleN = 1000)
p <- plotFeatureBoundaryCoverage(cvgF = cvgF, 
                                 cvgT = cvgT, 
                          featureName = 'transcript')   
                                                          

RCAS documentation built on Nov. 8, 2020, 8:03 p.m.