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GenotypeComparator

Compares the allele and genotype differences between two sets of genotype frequencies. Columns of the output statistics are described in the LaTeX documentation of this component.

Version 1.7
Bundle microarray
Categories SNP
Authors Marko Laakso (Marko.Laakso@Helsinki.FI)
Issue tracker View/Report issues
Requires commons-math3-3.2.jar (jar) ; microarray.jar (jar) ; installer (bash)
Source files component.xml
Usage Example with default values

Inputs

Name Type Mandatory Description
caseF SNPFreq Mandatory A table of case genotype frequencies
controlF SNPFreq Mandatory A table of control genotype frequencies

Outputs

Name Type Description
statistics CSV A table of genotype frequencies

Parameters

Name Type Default Description
CILimit float 0.99 Coverage of the confidence intervals.
PLimit float 1.00 Do not generate output for markers where all p-values are greater than this limit.
RiskType string "RiskRatio" Risk comparison method. Only RiskRatio and OddsRatio are correct values.
skipCI1 boolean false Do not generate output for markers where each confidence interval includes one.

Test cases

Test case Parameters IN
caseF
IN
controlF
OUT
statistics
case1 (missing) caseF controlF statistics

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