plotSizeDistribution: Plot the distribution of cluster sizes

In FedericoComoglio/wavClusteR: Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

Description

Produce an histogram of cluster sizes

Usage

plotSizeDistribution( clusters, showCov = FALSE, ... )

Arguments

clusters	GRanges object containing individual clusters as identified by the getClusters function
showCov	logical, if TRUE a scatter plot of average cluster coverage vs. cluster size is shown along with a loess fit. Default is FALSE.
...	Additional parameters to be passed to the hist function

Value

Called for its effect, returns a histogram.

Author(s)

Federico Comoglio

See Also

getClusters

Examples

require(BSgenome.Hsapiens.UCSC.hg19)

data( model, package = "wavClusteR" ) 

filename <- system.file( "extdata", "example.bam", package = "wavClusteR" )
example <- readSortedBam( filename = filename )
countTable <- getAllSub( example, minCov = 10, cores = 1 )
highConfSub <- getHighConfSub( countTable, supportStart = 0.2, supportEnd = 0.7, substitution = "TC" )
coverage <- coverage( example )
clusters <- getClusters( highConfSub = highConfSub, 
                         coverage = coverage, 
                         sortedBam = example, 
	                        threshold = 2 ) 

fclusters <- filterClusters( clusters = clusters, 
		             highConfSub = highConfSub, 
        		     coverage = coverage,
			     model = model, 
			     genome = Hsapiens, 
		             refBase = 'T', 
		             minWidth = 12 )
plotSizeDistribution(fclusters, breaks = 30, col = 'skyblue2')

FedericoComoglio/wavClusteR documentation built on Oct. 29, 2020, 2:44 p.m.