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BreakpointVisualizer

Visualizes genomic breakpoints resulting from copy-number aberrations (amplifications and deletions) and chromosomal rearrangements (translocations and inversions).

Creates a bar plot that shows number of breakpoints in each chromosome (grouped by breakpoint type) and for each chromosome a figure with a scatter plot and a histogram of the locations of the breakpoints.

WARNING: Loads the whole data into memory twice, so beware of using big data.

Also note that this is an early version, and assumes specific columns for the inputs.

Version 0.1.1
Bundle sequencing
Categories VariationAnalysis
Authors Viljami Aittomaki (viljami.aittomaki@helsinki.fi)
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Requires R ; ggplot2 (R-package) ; gridExtra (R-package)
Source files component.xml BreakpointVisualizer.r
Usage Example with default values

Inputs

Name Type Mandatory Description
cna CSV Mandatory Copy-number aberration data.
rearrangements CSV Mandatory Chromosomal rearrangement data, i.e. translocations and inversions.

Outputs

Name Type Description
report Latex The visualizations as a Latex fragment.

Parameters

Name Type Default Description
binwidth int 100000 Width of bins for histogram in bp. Small bins can be slow to compute.

Generated 2018-12-16 07:42:11 by Anduril 2.0.0