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Up: Component summary
Component
PairCorrelationCalculates correlations for the row pairs.
| Version | 1.1 |
|---|---|
| Bundle | tools |
| Categories | Analysis |
| Authors | Marko Laakso (Marko.Laakso@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Source files | component.xml PairCorrelation.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| data | Matrix | Mandatory | Rows of entities and columns of experiments / replicates |
| pairs | CSV | Mandatory | A table with two columns providing pairs of row identifiers for the data matrix |
Outputs| Name | Type | Description |
|---|---|---|
| stats | CSV | Correlations of the pairs |
| skipped | IDList | These entities were skipped due the lack of data |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| method | string | "cor-spearman" | Type of the correlation test: "cor-pearson" or "cor-spearman". |
| pLimit | float | 0.05 | Correlations with a p-value less or equal to this are accepted |
| pairCol1 | string | "" | Column name for the first identifier in the pairs input. An empty string refers to the first column. |
| pairCol2 | string | "" | Column name for the second identifier in the pairs input. An empty string refers to the second column. |
| rDownMax | float | -0.5 | Correlations less or equal to this limit are accepted |
| rUpMin | float | 0.5 | Correlations greater or equal to this limit are accepted |
Test cases| Test case | Parameters▼ | IN data |
IN pairs |
OUT stats |
OUT skipped |
|
|---|---|---|---|---|---|---|
| case1 | properties | data | pairs | stats | skipped | |
|
pLimit = 0.8 |
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