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RefSNPAnnotator

Fetches 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,
keyColumn =

case2-emptyInput properties rsIDs annotations geneChanges databases

dataset = mmusculus_snp,
keyColumn = rsID

case3-emptyOutput properties rsIDs annotations geneChanges databases

dataset = mmusculus_snp,
keyColumn = rsID

case4-invalidKeyColumn properties rsIDs (expecting failure) (expecting failure) (expecting failure)

keyColumn = foo

case5-invalidDataset properties rsIDs (expecting failure) (expecting failure) (expecting failure)

dataset = invaliddataset_snp


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