Up: Component summary
Up: Component summary
Component
SNPHelistinReaderImports genotype data from a SNPHelistin database. SNPHelistin and its documentation can be found from the home page of asser.jar.
| Version | 1.2 |
|---|---|
| Bundle | microarray |
| Categories | Data Import SNP |
| Authors | Marko Laakso (Marko.Laakso@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | SNPHelistin ; microarray.jar (jar) |
| Source files | component.xml |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| sampleNames | IDList | Mandatory | List of sample names of interest. |
| markerNames | IDList | Mandatory | List of SNP identifiers of interest. |
| config | Properties | Mandatory | Connection parameters for SNPHelistin. |
Outputs| Name | Type | Description |
|---|---|---|
| genotypes | SNPMatrix | SNPHelistin genotype output. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| errorSymbol | string | "ERR" | Symbol for failed measurements. You may for example use 'NA' value in order consider them equal to missing values. |
| skipUnknown | boolean | false | Ignore unknown samples and do not process them. If the parameter is false then the program fails for these samples. |
Test cases| Test case | Parameters▼ | IN sampleNames |
IN markerNames |
IN config |
OUT genotypes |
|
|---|---|---|---|---|---|---|
| case1 | (missing) | sampleNames | markerNames | config | genotypes | |
| case2 | properties | sampleNames | markerNames | config | genotypes | |
|
skipUnknown=true, |
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