Up: Component summary Function

AffySNPFetch

Fetches SNP rs-numbers from Ensembl based on Affy SNP-ids.

Version 1.0
Bundle microarray
Categories Annotation SNP Affy
Authors Riku Louhimo (Riku.Louhimo@Helsinki.FI)
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Source files component.xml function.scala
Usage Example with default values

Inputs

Name Type Mandatory Description
markernames CSV Mandatory A list of marker ids that have a synonym in Ensembl variation database. The column name for the column containing the markers is defined in parameter columnIn.
connection Properties Mandatory Database connection is defined in this file. Definitions of the parameters database.url, database.timeout, database.recycle, and database.driver can be found from the documentation of Korvasieni.

Outputs

Name Type Description
rsnumbers CSV SNPIDs as rs-numbers.

Parameters

Name Type Default Description
columnIn string "markers" Column name of the CSV file containing the IDs of interest.

Test cases

Test case Parameters IN
markernames
IN
connection
OUT
rsnumbers
case1 properties markernames connection rsnumbers

columnIn=AffyID

case2 (missing) markernames connection rsnumbers

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