Up: Component summary Component

AlleleCounter

Calculates genotype frequencies of a SNPMatrix. This component tests each SNP for its Hardy-Weinberg equilibrium. If there are NA values, the frequencies of missing value per sample in the input file are calculated.

Version 1.2.1
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)
Source files component.xml
Usage Example with default values

Inputs

Name Type Mandatory Description
genotypes SNPMatrix Mandatory SNPHelistin genotype output.

Outputs

Name Type Description
frequencies SNPFreq A table of genotype frequencies
naDist CSV Distribution of missing values. This table contains two columns (numberOfNAs and freq).

Parameters

Name Type Default Description
dels boolean false Accept homozygous deletions (--) as a possible genotype. They are considered as missing values by default.
naLimit float 1.0 Skip markers where one minus call rate exceeds this limit.
skip float -1.00 Drop markers with a relative minor allele frequency lower than this limit. Use negative values to inactivate this limit.

Test cases

Test case Parameters IN
genotypes
OUT
frequencies
OUT
naDist
case1 (missing) genotypes frequencies naDist
case2 properties genotypes frequencies naDist

dels = true,
naLimit = 0.2,
skip = 0.3


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