Up: Component summary
Up: Component summary
Component
SpatialContrastFinds two spatial regions in expression data that have a maximum contrast in average expression value. The regions correspond to the lowest and highest expression regions on the chip.
| Version | 1.0 |
|---|---|
| Bundle | microarray |
| Categories | Quality Control |
| Authors | Kristian Ovaska (kristian.ovaska@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | R |
| Source files | component.xml SpatialContrast.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| expr | LogMatrix | Mandatory | Expression data. |
| geneAnnotation | AnnotationTable | Mandatory | Contains location information for the probes in columns 'Row' and 'Col'. |
Outputs| Name | Type | Description |
|---|---|---|
| report | Latex | Spatial region report. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| margin | int | 0 | Number of probes on each side (left, upper, right, lower) that are left out of the analysis. |
| regionArea | float | 1000 | The regions must contain at least this many probes. |
Test cases| Test case | Parameters▼ | IN expr |
IN geneAnnotation |
OUT report |
||
|---|---|---|---|---|---|---|
| case1 | properties | expr | geneAnnotation | report | ||
|
regionArea=16 |
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| case2 | properties | expr | geneAnnotation | report | ||
|
regionArea=9, |
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