Up: Component summary
Up: Component summary
Component
FSomMetaClusteringCreates self-organizing maps of cytometry data with FlowSOM algorithm and meta clusters the data based on 100 fSOM-maps with consensus clustering. Performs quickly even for large datasets.
| Version | 1.0 |
|---|---|
| Bundle | tools |
| Categories | Clustering |
| Authors | Oskari Lehtonen (oskari.lehtonen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | R (R-package) ; FlowSOM (R-package) ; flowCore (R-package) ; ConsensusClusterPlus (R-package) |
| Source files | component.xml fSomMetaClustering.R |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | CSV | Mandatory | Input data, tab separated file. Numeric with column names |
Outputs| Name | Type | Description |
|---|---|---|
| out | CSV | Data frame of cluster labels. |
| fullData | CSV | Membership probability for each row in the input data |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| columnsToRemove | string | "" | Comma separated list of names of columns not to be used in clustering. Useful if you want to ignore some attribute in the data while clustering. |
| k | int | 10 | The number of clusters. Max 100. |
| seed | int | 1234 | Set the seed for the algorithms to make the results reproducible |
Test cases| Test case | Parameters▼ | IN in |
OUT out |
OUT fullData |
||
|---|---|---|---|---|---|---|
| case1 | properties | in | out | fullData | ||
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seed=1234, |
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