Up: Component summary
Up: Component summary
Component
CreateSQLiteIDsFor a subset of genes, create a file with additional reference IDs. Required for easy and efficient merging of TPdb info.
| Version | 0.1 |
|---|---|
| Bundle | sequencing |
| Categories | DEG smallRNA |
| Authors | Katherine Icay (katherine.icay@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | biomaRt (R-bioconductor) |
| Source files | component.xml SQLiteDB_xIDs.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| geneList | CSV | Mandatory | Tab-delimited CSV file with headers and at least one column containing gene IDs to look up. |
Outputs| Name | Type | Description |
|---|---|---|
| wIDs | CSV | Input file content with additional columns containing the listed reference IDs in the parameters. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| attrTypes | string | "" | Comma-separated list of associated gene IDs/attributes to retrieve. |
| biomart_dataset | string | "hsapiens_gene_ensembl" | Ensembl biomart dataset to use. |
| keyCol | string | "" | Column name of the input geneList to look up associated IDs for. |
| keyType | string | "ensembl_transcript_id" | BiomaRt reference type of the keyCol. For reference, see a list of available attributes in hsapiens_gene_ensembl. |
| useMart_host | string | "" | Genome build and version to pull references from. For example, "jun2013.archive.ensembl.org" retrieves IDs available in Ensembl 72. See Ensembl Archives to find the correct host URL. |
Test cases| Test case | Parameters▼ | IN geneList |
OUT wIDs |
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|---|---|---|---|---|---|---|
| case1 | properties | geneList | wIDs | |||
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keyCol=mRNA, |
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