Up: Component summary
Up: Component summary
Component
AlleleCounterCalculates 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, |
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