Up: Component summary
Up: Component summary
Component
GeneInfoPrints detailed information on single genes. The information includes expression values and optional annotation.
| Version | 1.0 |
|---|---|
| Bundle | microarray |
| Categories | Latex |
| Authors | Kristian Ovaska (kristian.ovaska@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | R |
| Source files | component.xml GeneInfo.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| expr1 | LogMatrix | Mandatory | Expression matrix 1. |
| expr2 | LogMatrix | Optional | Expression matrix 2. |
| expr3 | LogMatrix | Optional | Expression matrix 3. |
| geneAnnotation | AnnotationTable | Optional | Annotation for the genes. The columns specified with the parameter annotationColumns are copied in the report. |
| groups | SampleGroupTable | Optional | Sample group table that is used to fetch the human-readable name for sample groups. If not given, the group ID is used instead in the report. |
Outputs| Name | Type | Description |
|---|---|---|
| report | Latex | Latex section that contains one section for each gene. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| annotationColumns | string | "" | Comma-separated list of column names in geneAnnotation that are copied into the report. |
| exprColumns | string | "*" | Expression column names to be included. The special value * includes all columns. |
| geneConversionColumn | string | "" | Column name in geneAnnotation that is used to convert reported gene names. |
| geneIDs | string | (no default) | Comma-separated list of gene/probe IDs that refer to the ID column of the expression matrix. |
Test cases| Test case | Parameters▼ | IN expr1 |
IN expr2 |
IN expr3 |
IN geneAnnotation |
IN groups |
OUT report |
|---|---|---|---|---|---|---|---|
| case1 | properties | expr1 | expr2 | (missing) | geneAnnotation | groups | (missing) |
|
geneIDs=P1,P3,P4, |
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