plotWindow: Plot read counts within a genomic region

In ChIPseqR: Identifying Protein Binding Sites in High-Throughput Sequencing Data

Description

Read count within a selected region of the genome are plotted, optionally together with binding site score and location of predicted binding sites.

Usage

.plotWindow(data, chr, center, score, width=2000, bind, start, end, bind.col=3, score.type='l',	
	xlab=NULL, ylab="Read count", cutoff=TRUE, offset = 1, ...)

Arguments

data	Object of class ReadCounts or a list of read counts.
chr	A character string or numeric index identifying the the chromosome on which the region is located.
center	Numeric value giving the center of the region on chromosome 'chr' that should be plotted.
score	An object of class BindScore, may be missing.
width	Width of the window to plot. The plotted region will be [center - width/2, center + width/2].
bind	Length of binding site, ignored if 'score' is missing.
start	Start of plotting window (may be used together with end instead of center).
end	End of plotting window (may be used together with start instead of center).
bind.col	Color used to indicate location of binding sites, ignored if 'score' is missing.
score.type	Plotting type to use for score, ignored if 'score' is missing.
xlab	X-axis label. This defaults to a description of the genomic location constructed from 'chr', 'center' and 'width'
ylab	Y-axis label.
cutoff	Logical indicating whether the significance threshold used to predict binding site locations should be indicated by a horizontal line in the plot.
offset	Position on chromosome chr corresponding to the first read count in data.
...	Further arguments to plot.

Details

If 'score' is present the binding site score is plotted on top of read counts. Scores are rescaled to lie between 0 and the maximum number of reads in the window. A corresponding scale is added to the right hand axis.

Value

Called for its side effect.

Author(s)

Peter Humburg

ChIPseqR documentation built on Nov. 8, 2020, 6:49 p.m.