hypergate {hypergate}

hypergate

Description

Finds a hyperrectangle gating around a population of interest

Usage

hypergate(xp, gate_vector, level, delta_add = 0, beta = 1, verbose = FALSE)

Arguments

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.

See Also

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

Examples

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)