Up: Component summary Component

SNPHelistinReader

Imports genotype data from a SNPHelistin database. SNPHelistin and its documentation can be found from the home page of asser.jar.

Version 1.2
Bundle microarray
Categories Data Import SNP
Authors Marko Laakso (Marko.Laakso@Helsinki.FI)
Issue tracker View/Report issues
Requires SNPHelistin ; microarray.jar (jar)
Source files component.xml
Usage Example with default values

Inputs

Name Type Mandatory Description
sampleNames IDList Mandatory List of sample names of interest.
markerNames IDList Mandatory List of SNP identifiers of interest.
config Properties Mandatory Connection parameters for SNPHelistin.

Outputs

Name Type Description
genotypes SNPMatrix SNPHelistin genotype output.

Parameters

Name Type Default Description
errorSymbol string "ERR" Symbol for failed measurements. You may for example use 'NA' value in order consider them equal to missing values.
skipUnknown boolean false Ignore unknown samples and do not process them. If the parameter is false then the program fails for these samples.

Test cases

Test case Parameters IN
sampleNames
IN
markerNames
IN
config
OUT
genotypes
case1 (missing) sampleNames markerNames config genotypes
case2 properties sampleNames markerNames config genotypes

skipUnknown=true,
errorSymbol=--


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