Up: Component summary
Up: Component summary
Component
ClusterFilteringFilters columns and/or rows from by clusters using flexible criteria. Possible to filter clusters out by minimum number of events/cluster or by relative median/mean value of cluster centers.
| Version | 1.0 |
|---|---|
| Bundle | flowand |
| Categories | FlowCytometry |
| Authors | Erkka Valo (erkka.valo@helsinki.fI), Ping Chen (ping.chen@helsinki.fi), Anna-Maria Lahesmaa-Korpinen (anna-maria.lahesmaa@helsinki.fi) |
| Requires | R |
| Source files | component.xml ClusterFiltering.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| fcsDir | CSVList | Optional | A Directory containing CSV files that represent samples measured in FACS experiment. Rows represent cells and columns measured variables. Each file should contain one column representing clusters. |
| in | Array<CSV> | Optional | An array of CSV files for samples from a FACS experiment. |
Outputs| Name | Type | Description |
|---|---|---|
| filtered | CSVList | A Folder containing the filtered FCS files. |
| out | Array<CSV> | Array of filtered CSV files. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| clusterColumn | string | "" | The name of the column which contains cluster indexes. |
| combineMethod | string | "median" | The method used for combining intensities for each cluster. It can be 'median' or 'mean'. Note: filtering is done based on the combined data for each cluster. |
| filterColumn | string | "" | A comma-separated channel IDs based on which the filtering is done. If filtering is based on all channels, set it to '*'. |
| filterDiff | float | 0.0 | Difference of cluster center to median of all cluster centers. |
| minCellNumber | int | 10 | The minimum number of cells in a cluster. If a cluster contains cells less than this threshold, all the cells in the cluster will be removed. |
Test cases| Test case | Parameters▼ | IN fcsDir |
IN in |
OUT filtered |
OUT out |
|
|---|---|---|---|---|---|---|
| case1 | properties | fcsDir | (missing) | filtered | (missing) | |
|
minCellNumber=2, |
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| case2 | properties | fcsDir | (missing) | filtered | (missing) | |
|
minCellNumber=2, |
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| case3_mixedarray | properties | fcsDir | in | filtered | (missing) | |
|
minCellNumber=2, |
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