Up: Component summary
Up: Component summary
Function
AffySNPFetchFetches SNP rs-numbers from Ensembl based on Affy SNP-ids.
| Version | 1.0 |
|---|---|
| Bundle | microarray |
| Categories | Annotation SNP Affy |
| Authors | Riku Louhimo (Riku.Louhimo@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Source files | component.xml function.scala |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| markernames | CSV | Mandatory | A list of marker ids that have a synonym in Ensembl variation database. The column name for the column containing the markers is defined in parameter columnIn. |
| connection | Properties | Mandatory | Database connection is defined in this file. Definitions of the parameters database.url, database.timeout, database.recycle, and database.driver can be found from the documentation of Korvasieni. |
Outputs| Name | Type | Description |
|---|---|---|
| rsnumbers | CSV | SNPIDs as rs-numbers. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| columnIn | string | "markers" | Column name of the CSV file containing the IDs of interest. |
Test cases| Test case | Parameters▼ | IN markernames |
IN connection |
OUT rsnumbers |
||
|---|---|---|---|---|---|---|
| case1 | properties | markernames | connection | rsnumbers | ||
|
columnIn=AffyID |
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| case2 | (missing) | markernames | connection | rsnumbers | ||