Up: Component summary
Up: Component summary
Component
RefSNPAnnotatorFetches annotations for given SNP rsID's with biomaRt.
Outputs a table with general annotations, where associations with multiple genes (for one SNP) are listed as a comma separated list. Also outputs a CSV with change effects on genes for SNPs in coding regions. Multiple associations (for one SNP) are listed as separate entries with the same refsnp_id.
Logs rsID's that return no match.
| Version | 1.1.3 |
|---|---|
| Bundle | microarray |
| Categories | SNP Annotation |
| Authors | Viljami Aittomaki (viljami.aittomaki@helsinki.fi), Marko Laakso (Marko.Laakso@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | R ; biomaRt (R-bioconductor) |
| Source files | component.xml RefSNPAnnotator.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| rsIDs | CSV | Mandatory | List of rsID's for fetching annotations. |
Outputs| Name | Type | Description |
|---|---|---|
| annotations | AnnotationTable | General annotations as a Table. Contains columns: refsnp_id, allele, chr_name, chrom_start, chrom_strand, ensembl_gene_stable_id, validated |
| geneChanges | CSV | Gene change effects as a CSV. Contains columns: refsnp_id, ensembl_gene_stable_id, ensembl_peptide_shift, consequence_type_tv, consequence_allele_string |
| databases | Properties | A properties file which lists the database versions that biomaRt currently uses and the dataset (organism) used for fetching annotations. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| dataset | string | "hsapiens_snp" | Dataset to get annotations from. Different species have their own datasets. Example values include "hsapiens_snp" and "mmusculus_snp". See biomaRt documentation on how to list available datasets in R. |
| keyColumn | string | "" | Name of the key column withing sourceKeys file or an empty string for the first column. |
Test cases| Test case | Parameters▼ | IN rsIDs |
OUT annotations |
OUT geneChanges |
OUT databases |
|
|---|---|---|---|---|---|---|
| case1 | properties | rsIDs | annotations | geneChanges | databases | |
|
dataset = hsapiens_snp, |
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| case2-emptyInput | properties | rsIDs | annotations | geneChanges | databases | |
|
dataset = mmusculus_snp, |
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| case3-emptyOutput | properties | rsIDs | annotations | geneChanges | databases | |
|
dataset = mmusculus_snp, |
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| case4-invalidKeyColumn | properties | rsIDs | (expecting failure) | (expecting failure) | (expecting failure) | |
|
keyColumn = foo |
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| case5-invalidDataset | properties | rsIDs | (expecting failure) | (expecting failure) | (expecting failure) | |
|
dataset = invaliddataset_snp |
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