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AutoGating

Automatically 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.

Generated 2018-12-12 07:42:05 by Anduril 2.0.0