Up: Component summary Function

RegionOverlap

Produces 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
case1 (missing) regions1 regions2 regions
case2 properties regions1 regions2 regions

takeDiff = true


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