plot-methods

plot.ExomeDepth

plot,ANY-method

plot,ExomeDepth,ANY-method

plot,ExomeDepth-method

character, Name of the sequence/chromosome of the region to
 plot (for example "chr5" would be typical)

sequence

numeric of size 2, start and end position of the region
 to plot

xlim

numeric of size 2, range for the y-axis

ylim

numeric, minimum number of reads in the reference set to
 display a point in the plot

count.threshold

logical, Should the gene information (obtained from
 the annotation data) be plotted under the read depth plot?

with.gene

character, Colour for the line displaying the read depth
 ratio for each exon

Plot function for the ExomeDepth class

methods

Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.

Vincent Plagnol

ExomeDepth

Calls Copy Number Variants from Targeted Sequence Data

plot-methods function

<dl class="dl-horizontal">
<dt><code>signature(x = "ExomeDepth", sequence, xlim, ylim = NULL,
 count.threshold = 10, ylab = 'Observed by expected read ratio', xlab
 = '', type = 'b', pch = '+', with.gene = FALSE, col =
 'red',...)</code></dt><dd></dd></dl>

Methods

Plotting function for ExomeDepth objects — plot-methods

<dl class='dl-horizontal'>
<dt><code>signature(x = "ExomeDepth", sequence, xlim, ylim = NULL,
 count.threshold = 10, ylab = 'Observed by expected read ratio', xlab
 = '', type = 'b', pch = '+', with.gene = FALSE, col =
 'red',...)</code></dt><dd></dd></dl>

plot-methods: Plotting function for ExomeDepth objects

Description

Arguments

Methods