Up: Component summary
Up: Component summary
Component
BreakpointVisualizerVisualizes 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) |
| Issue tracker | View/Report issues |
| 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. |