REDseq (version 1.18.0)

plotCutDistribution: plot cut frequencies of RE sites along a given chromosome

Description

plot cut frequencies of RE sites along a chromosome, which gives a bird-eye view of genome-wide frequent-cut regions and RE inaccessible regions.

Usage

plotCutDistribution(assignedSeqs,REmap, chr="chr1",xlim, 
title="RE cut frequency distribution",
xlab="Chromosome Location (bp)",ylab="Frequency", 
round=TRUE, n.sequence)

Arguments

assignedSeqs

result returned from assignSeq2REsite

REmap

REmap used in assignSeq2REsite and generated from buildREmap

chr

chromosome to be plotted

xlim

range of x to be plotted

title

an overall title for the plot

xlab

a title for the x axis

ylab

a title for the y axis

round

TRUE: the sum of the weight is rounded up if the fraction part is greater than 0.5. FALSE: as it is.

n.sequence

total uniquely mapped sequences in the dataset for estimating the expected count for each RE site. If omitted, the expected count for each RE site will be set as 1 as default.

See Also

assignSeq2REsite, distanceHistSeq2RE

Examples

	library(REDseq)
	data(example.assignedREDseq)
	data(example.map)
	plotCutDistribution(example.assignedREDseq,example.map,
chr="2", xlim =c(3012000, 3020000))