Up: Component summary
Up: Component summary
Component
FlowClustModelingModeling FACS data using flowClust library
| Version | 0.1 |
|---|---|
| Bundle | flowand |
| Categories | FlowCytometry |
| Authors | Anna-Maria Lahesmaa-Korpinen (anna-maria.lahesmaa@helsinki.fi) |
| Requires | R ; flowCore (R-bioconductor) ; flowClust (R-bioconductor) ; geneplotter (R-bioconductor) |
| Source files | component.xml FlowClustModeling.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| fcsDir | CSVList | Mandatory | Directory for FCS files in CSV format. |
Outputs| Name | Type | Description |
|---|---|---|
| clusters | CSVList | Clustered data files, with last column as cluster number. |
| report | Latex | Visualization of compensation results. Contains jpeg for each original file. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| channelsToCluster | string | (no default) | A comma-separated list of channel/antibody numbers, to be clustered (e.g., "SSC.A,CD4,CD3,CD45"). |
| clusterIDColName | string | "cluster" | The name of the column in the clusters output which contains the cluster IDs of the rows. |
| height | float | 250 | Height of plot per channel in px. |
| keepOriginalChannelNames | boolean | false | If true, original channel names are kept. Usually these are the antibody names. If false, channel names are replaced with the descriptions of the channels, if they exist. These are the names of the proteins targeted by the antibodies. |
| level | float | 0.9 | A numeric value between 0 and 1 specifying the threshold quantile level used to call a point an outlier. The default is 0.9, meaning that any point outside the 90% quantile region will be called an outlier. |
| maxClusters | int | 2 | An integer indicating the maximum number of clusters. |
| minClusters | int | 1 | An integer indicating the minimum number of clusters. |
| numIterations | int | 100 | The maximum number of EM iterations. |
| pagebreak | boolean | false | Tells if the result document should start with a page break. |
| width | float | 250 | Width of plot per channel in px. |
Test cases| Test case | Parameters▼ | IN fcsDir |
OUT clusters |
OUT report |
||
|---|---|---|---|---|---|---|
| case1 | properties | fcsDir | clusters | report | ||
|
channelsToCluster=FSC.H,SSC.H |
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