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 |
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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 |
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. |
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. |
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 case | Parameters▼ | IN exprMatrix |
IN cnaMatrix |
IN exprAnnotation |
OUT integrationResults |
OUT cghResults |
OUT annotations |
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case1 | properties | exprMatrix | cnaMatrix | exprAnnotation | integrationResults | cghResults | annotations |
fraction=0.95, |
|||||||
case2 | properties | exprMatrix | cnaMatrix | exprAnnotation | integrationResults | cghResults | annotations |
fraction=0.96 |