Up: Component summary
Up: Component summary
Component
PeakScoreCalculates a cumulative score for each gene having some regions assigned to it. The score is based on the distance of the region. The closer or the more assigned regions a gene has the better score it will obtain.
For each gene (g) assignment (p) with an optional score (w) the output score_p is w*(s-distance)/s or w*(e^(-distance/s)) depending on the selected formula (linear or exponential). The cumulative score is incremented if score_p > 0: score_g=score_g+score_p.
| Version | 1.2 |
|---|---|
| Bundle | microarray |
| Categories | Annotation Short-read Sequencing |
| Authors | Marko Laakso (Marko.Laakso@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | microarray.jar (jar) |
| Source files | component.xml |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | CSV | Mandatory | Distances of the genes |
Outputs| Name | Type | Description |
|---|---|---|
| out | AnnotationTable | Table that contains the gene IDs and the corresponding scores |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| distColumn | string | (no default) | Name of the distance column in input |
| formula | string | "linear" | Selection of the score function (exponential or linear) |
| idColumn | string | (no default) | Name of the identifier column in input |
| minScore | float | 1.0 | Genes must obtain at least this score to be listed in output. |
| peaksColOut | string | "peaks" | Name of the output column, which contains the peak counts |
| s | float | 100000 | Scaling term for the distances that is the maximum distance |
| scoreColOut | string | "score" | Name of the output column, which contains the gene scores |
| scoreColumn | string | "" | Column name for the peak scores or an empty string for constant one |
Test cases| Test case | Parameters▼ | IN in |
OUT out |
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|---|---|---|---|---|---|---|
| case1 | properties | in | out | |||
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distColumn = distance, |
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| case2 | properties | in | out | |||
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scoreColumn = score, |
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| case3 | properties | in | out | |||
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formula = exponential, |
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