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'
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.