The Hypergate operator automatically defines a one vs. rest labelling of cytometry data. It analyzes expression values across markers to define a gate that would describe a population of interest defined by the user.
This operator is a wrapper for the hypergate R package (version 0.8.5).
| Input projection | . |
|---|---|
row |
represents the variables (markers) |
column |
represents the observations (cells/events) |
y-axis |
represents the measurement values |
| Input parameters | . |
|---|---|
high_expression |
numeric, quantile threshold for highly expressed markers, default is 0.7 |
low_expression |
numeric, quantile threshold for lowly expressed markers, default is 0.3 |
expressed_marker |
string, comma-separated list of markers that should be highly expressed, default is "" |
not_expressed_marker |
string, comma-separated list of markers that should be lowly expressed, default is "" |
| Output relations | . |
|---|---|
hypergate_member |
numeric, 1 if the event is inside the hypergate, 0 if outside |
The operator takes the following steps:
- Identifies a population of interest based on marker expression thresholds
- Applies the hypergate algorithm to find an optimal hyperrectangular gate
- Returns gate membership for each event
The population of interest is defined by:
- Events with expression values above the
high_expressionquantile for markers listed inexpressed_marker - Events with expression values below the
low_expressionquantile for markers listed innot_expressed_marker
At least one marker must be specified in either expressed_marker or not_expressed_marker.
- Hypergate R package
- Becht, E., Simoni, Y., Coustan-Smith, E. et al. Reverse-engineering flow-cytometry gating strategies for phenotypic labelling and high-performance cell sorting. Nat Biotechnol 39, 529–539 (2021). https://doi.org/10.1038/s41587-020-00744-z