PlotSpatialDistribution: Plot spatial distribution of loci from a 'txLoc' object.

In mevers/RNAModR: Functional Analysis of RNA Modifications

Description

Plot spatial distribution of loci from a txLoc object within every transcript region.

Usage

PlotSpatialDistribution(txLoc, nbreaks = 100, absolute = FALSE,
  binWidth = NULL, posMax = 1000, doBootstrap = TRUE, ...)

Arguments

txLoc	A txLoc object.
nbreaks	Number of spatial bins. Default is 100.
absolute	Plot spatial distribution in absolute coordinates. Default is FALSE.
binWidth	Spatial bin width. Overrides nbreaks if not NULL.
posMax	If absolute == TRUE, show spatial distribution within a window given by posMax from the 5'/3' position of the transcript feature. Default is 1000 nt.
doBootstrap	Calculate 95 sites within transcript region. Default is TRUE.
...	Additional parameters passed to plot.

Value

NULL.

Author(s)

Maurits Evers, [e-mail]

Examples

## Not run: 
bedFile <- system.file("extdata",
                       "miCLIP_m6A_Linder2015_hg38.bed",
                       package = "RNAModR")
sites <- ReadBED(bedFile)
posSites <- SmartMap(sites, id = "m6A", refGenome = "hg38")
PlotSpatialDistribution(posSites)
PlotSpatialDistribution(posSites,
                        absolute = TRUE,
                        filter = c("5'UTR", "CDS", "3'UTR"),
                        ylim = c(0, 200))

## End(Not run)

mevers/RNAModR documentation built on Nov. 17, 2019, 9:11 a.m.