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GSVDIntegrator

Extracts variation patterns from two matrices based on the generalized singular value decomposition. One input matrix contains values from a CGH microarray while the other contains expression values.

Outputs contain those rows of the matrices that show similar patterns of variation between the two input matrices.

This component utilizes the GSVD integrator matlab library.

Version 1.0.1
Bundle microarray
Categories Integration
Authors Riku Louhimo (Riku.Louhimo@Helsinki.FI)
Issue tracker View/Report issues
Requires Matlab
Source files component.xml scaleData.m gsvdShaving.m gsvdIntegrator.m execute.m
Usage Example with default values

Inputs

Name Type Mandatory Description
exprMatrix LogMatrix Mandatory Matrix of normalized expression values.
cnaMatrix LogMatrix Mandatory Matrix of normalized copy number values.
exprAnnotation AnnotationTable Mandatory Annotations for the probes.

Outputs

Name Type Description
integrationResults CSV Result genes from the integration.
cghResults CSV Array CGH intensitites for the result genes from the integration.
annotations CSV Result gene annotations from the integration.

Parameters

Name Type Default Description
direction string "zero" The direction of the projection. One of "min", "max", or "zero".
fraction float 0.95 The fraction of input rows to keep after each iteration of the shaving algorithm.
numRem int 600 The minimum number of input rows to retain after the execution of the shaving algorithm.

Test cases

Test case Parameters IN
exprMatrix
IN
cnaMatrix
IN
exprAnnotation
OUT
integrationResults
OUT
cghResults
OUT
annotations
case1 properties exprMatrix cnaMatrix exprAnnotation integrationResults cghResults annotations

fraction=0.95,
direction=max,
numRem=380

case2 properties exprMatrix cnaMatrix exprAnnotation integrationResults cghResults annotations

fraction=0.96


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