Up: Component summary
Up: Component summary
Component
AutoGatingAutomatically gate cell populations. Gating is done based rules defined in input file "rule".
| Version | 1.0 |
|---|---|
| Bundle | flowand |
| Categories | FlowCytometry |
| Authors | Ping Chen (ping.chen@helsinki.fi) |
| Requires | R ; sqldf (R-package) |
| Source files | component.xml AutoGating.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| rule | CSV | Mandatory | The rule setting for automatically gating. The file contains 7 columns (ID,Population,Quantile,Rank,Variable,Measure,Rule). 'ID' column stands for the index for the cell population under study; 'Population' demonstrates the cell population name; 'Quantile' column is for choosing clusters based on cell numbers; 'Rank' number is the order of cell population for gating; 'Variable' specifies the channels that gating is based on; 'Measure' supports 'range' or 'ratio' type; 'Rule' shows the gating rule for corresponding measurement. Note: If you use both 'range' and 'ratio' for gating a cell population, 'range' should be proceeded before 'ratio'. |
| clusters | CSVList | Optional | A directory containing clustering results for one or multiple samples. For one sample there should be multiple results corresponding to results with different number of clusters. One column in the CSV files should contain the cluster membership information for the row. |
| array | Array<CSV> | Optional | An array of CSV files which contain clustering results for one or multiple samples. For one sample there should be multiple results corresponding to results with different number of clusters. One column in the CSV files should contain the cluster membership information for the row. |
Outputs| Name | Type | Description |
|---|---|---|
| filtered | CSVList | A directory containing filtered clustering data with clusters identified as populations. |
| filteredArray | Array<CSV> | Array of filtered clustering data with clusters identified as populations. |
| population | CSVList | Automatically gated cell populations. |
| populationArray | Array<CSV> | Array of gated cell populations. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| clusterCol | string | "cluster" | The name of the column in the input clusterFiles which represents the cluster number of the rows. |
| cutOff | float | 0.1 | The distance cutoff for merging two clusters. If v (v = distance/maximun-distance) between two clusters is smaller than the cutoff value, two clusters will be merged into the same cell population. |
| p | float | 0.05 | P value for removing outliers in each cluster. |