hypergate | R Documentation |
Finds a hyperrectangle gating around a population of interest
hypergate(xp, gate_vector, level, delta_add = 0, beta = 1, verbose = FALSE)
xp |
an Expression matrix |
gate_vector |
A Categorical vector of length nrow(xp) |
level |
A level of gate_vector so that gate_vector == level will produce a boolean vector identifying events of interest |
delta_add |
If the increase in F after an optimization loop is lower than delta_add, the optimization will stop (may save computation time) |
beta |
Purity / Yield trade-off |
verbose |
Boolean. Whether to print information about the optimization status. |
channels_contributions
for ranking parameters within the output, reoptimize_strategy
for reoptimizing a output on a subset of the markers, plot_gating_strategy
for plotting an output, subset_matrix_hg
to apply the output to another input matrix, boolmat
to obtain a boolean matrix stating which events are filtered out because of which markers
data(Samusik_01_subset)
xp=Samusik_01_subset$xp_src[,Samusik_01_subset$regular_channels]
gate_vector=Samusik_01_subset$labels
hg=hypergate(xp=xp,gate_vector=gate_vector,level=23,delta_add=0.01)
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