flGetGateAssignments: Given a DensityData object with existing thresholds, returns...

In mlux86/flowLearn: flowLearn

Description

This method gates each cell and indicates whether it belongs to the given target population or not. For that, the method needs the original expression matrix.

Usage

flGetGateAssignments(densdat, exprs, fcs, population, negate = FALSE)

Arguments

densdat	The full DensityData object with density and densities and set/predicted thresholds.
exprs	A n*d expression matrix of the parent population where n is the number of cells and d is the number of channels. The channel indices correspond to the channelIdx values in densdat.
fcs	The name of the FCS file to consider. This is needed to filter the relevant entries in densdat.
population	The name of the population to gate. This is needed to filter the relevant entries in densdat.
negate	Whether the gated population should be negated/inverted, i.e. not the cells within the gate but out of it are considered.

Value

A vector of length n, indicating cell membership to the population of interest.

Examples

f <- unique(flData(flSampleDensdat)$fcs)[[1]]
flGetGateAssignments(flSampleDensdat, flSampleBcellEvaluationData[[f]]$parentExprs, f, 'bcell')

mlux86/flowLearn documentation built on May 29, 2019, 5:43 a.m.