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

In REDseq: Analysis of high-throughput sequencing data processed by restriction enzyme digestion

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.

Author(s)

Lihua Julie Zhu

See Also

assignSeq2REsite, distanceHistSeq2RE

Examples

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

REDseq documentation built on Nov. 8, 2020, 8:19 p.m.