Up: Component summary
Up: Component summary
Function
RegionOverlapProduces a list of overlapping DNA regions. This component can also produce the asymmetric set difference of the region sets. Overlapping regions represent the actual base pairs that overlap whereas the difference is based on the coordinates of the regions in region1 when not a single base pair is shared between the selected items of it and the region2.
| Version | 1.2 |
|---|---|
| Bundle | microarray |
| Categories | Short-read Sequencing |
| Authors | Marko Laakso (Marko.Laakso@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Source files | component.xml function.scala |
| Usage | Example with default values |
| Deprecated |
This component could be replaced by a modern approach. |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| regions1 | CSV | Mandatory | The first set of DNA regions |
| regions2 | CSV | Mandatory | The second set of DNA regions |
Outputs| Name | Type | Description |
|---|---|---|
| regions | CSV | Overlapping regions |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| chrColumn | string | "chr" | Column name for chromosome information |
| endColumn | string | "end" | Column name for the region ends |
| idColumn | string | "" | An optional column name for region identifiers |
| scoreColumn | string | "" | An optional column name for the region scores |
| scoreFunc | string | "max" | Join function for the region scores. Options are max (maximum), min (minumum) and avg (average). |
| startColumn | string | "start" | Column name for the region starts |
| strandColumn | string | "" | Column name for the DNA strand identifier |
| takeDiff | boolean | false | Produce asymmetric set difference regions1\regions2 instead of the overlap. |
Test cases| Test case | Parameters▼ | IN regions1 |
IN regions2 |
OUT regions |
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|---|---|---|---|---|---|---|
| case1 | (missing) | regions1 | regions2 | regions | ||
| case2 | properties | regions1 | regions2 | regions | ||
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takeDiff = true |
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