plotFeatureBoundaryCoverage: plotFeatureBoundaryCoverage

plotFeatureBoundaryCoverageR Documentation

plotFeatureBoundaryCoverage

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')   
                                                          

BIMSBbioinfo/RCAS documentation built on Feb. 7, 2024, 4:38 p.m.