plot.ExomeDepth: Plotting function for ExomeDepth objects

In drramki-chop/edm: Scalable workflow to identify copy Number variants from exome sequencing data

Description

Plot function for the ExomeDepth class

Arguments

x	ExomeDepth object
sequence	character, Name of the sequence/chromosome of the region to plot (for example "chr5" would be typical)
xlim	numeric of size 2, start and end position of the region to plot
ylim	numeric of size 2, range for the y-axis
count.threshold	numeric, minimum number of reads in the reference set to display a point in the plot
with.gene	logical, Should the gene information (obtained from the annotation data) be plotted under the read depth plot?
col	character, Colour for the line displaying the read depth ratio for each exon

Methods

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',...)

drramki-chop/edm documentation built on June 6, 2020, 8:48 a.m.