Up: Component summary
Up: Component summary
Component
SamSpectralSamSPECTRAL clustering of flow cytometry data as described by Zare et al (2010).
More info in Bioconductor documentation.
| Version | 1.1 |
|---|---|
| Bundle | flowand |
| Categories | FlowCytometry |
| Authors | Anna-Maria Lahesmaa-Korpinen (anna-maria.lahesmaa@helsinki.fi) |
| Requires | R ; SamSPECTRAL (R-bioconductor) ; Rmpi (R-package) |
| Source files | component.xml SamSpectral.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| list | CSVList | Optional | Location of the csv files to be clustered e.g. Preprocessed files in flow cytometry analysis . |
| in | Array<CSV> | Optional | An Array of CSV files to be clustered e.g. Preprocessed files in flow cytometry analysis. |
Outputs| Name | Type | Description |
|---|---|---|
| clusters | CSVList | csv files including the input data and one additional column presenting the clustering results. The numbers added to the input filenames represent the number of clusters found. |
| out | Array<CSV> | csv files including the input data and one additional column presenting the clustering results. The numbers added to the input filenames represent the number of clusters found. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| channelsToCluster | string | (no default) | A comma-separated list of column names or column numbers (e.g. channel names/ numbers in flow cytometry analysis), to be clustered. As for instance the value could be set as "1, 2, 3, 4, 5" or "FSC.A, SSC, ERK1, STAT1, CD4" . |
| clusterIDColName | string | "cluster" | The name of the column in the clusters output
which contains the cluster IDs of the rows. |
| separationFactor | float | 0.5 | This threshold controls to what extend clusters should be combined or kept separate. Normally, an appropriate value will fall in range 0.3-2. |
| sigma | int | 100 | A scaling parameter typically between 10...1000. It determines the "resolution" in the spectral clustering stage. By increasing it, more spectral clusters are identified. This can be useful when "small" population are aimed. |
Test cases| Test case | Parameters▼ | IN list |
IN in |
OUT clusters |
OUT out |
|
|---|---|---|---|---|---|---|
| case1 | properties | list | (missing) | clusters | (missing) | |
|
channelsToCluster=FSC-H,SSC-H, |
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| case2 | properties | list | in | clusters | (missing) | |
|
channelsToCluster=FSC-H,SSC-H, |
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