Up: Component summary
Up: Component summary
Component
IlluminaAnnotatorFetches genomic annotations for Illumina methylation and expression array probes.
| Version | 13.10 |
|---|---|
| Bundle | microarray |
| Categories | Annotation DNA Methylation |
| Authors | Riku Louhimo (Riku.Louhimo@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | FDb.InfiniumMethylation.hg19 (R-bioconductor) ; IlluminaHumanMethylation27k.db (R-bioconductor) ; illuminaHumanv3.db (R-bioconductor) ; illuminaHumanv4.db (R-bioconductor) |
| Source files | component.xml IlluminaAnnotator.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | CSV | Mandatory | A list of Illumina probe ids. |
Outputs| Name | Type | Description |
|---|---|---|
| out | CSV | Table of annotations defined by 'types' for input probes. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| arrayType | string | (no default) | Array type. One of 'v4', '450' or '27'. |
| keyColumn | string | "" | Name of column in 'csv' containing probe ids or an empty string for the first column. |
| targetDB | string | "ENSEMBL,SYMBOL" | Comma-separated list annotation types. Possible values and their descriptions are listed here. Defaults to Ensembl GeneId and GeneName. |
Test cases| Test case | Parameters▼ | IN in |
OUT out |
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|---|---|---|---|---|---|---|
| case1 | properties | in | out | |||
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arrayType = 450 |
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| case2 | properties | in | out | |||
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arrayType = 450, |
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| case3 | properties | in | out | |||
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arrayType = v4 |
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