gatingMatrix: Apply gating on the matrix data

In JhuangLab/CytoTree: A Toolkit for Flow And Mass Cytometry Data

Description

Apply gating on the matrix data

Usage

gatingMatrix(x, lower.gate = NULL, upper.gate = NULL)

Arguments

x	matrix
lower.gate	vector. Gating parameter, the name of the vector is the marker name, and the value of the vector is the lower bound of gating cutoff.
upper.gate	vector. Gating parameter, the name of the vector is the marker name, and the value of the vector is the upper bound of gating cutoff.

Value

a matrix

Examples

par(mfrow=c(1,2))
x <- matrix(rnorm(200, 3, 1), nrow = 100, ncol = 2)
colnames(x) <- c("CD34", "CD43")
plot(x[, "CD34"], x[, "CD43"], main = "Before gating")

lower.gate = c(CD34 = 2, CD43 = 3)
upper.gate = c(CD34 = 4, CD43 = 5)

x <- gatingMatrix(x, lower.gate = lower.gate, upper.gate = upper.gate)
plot(x[, "CD34"], x[, "CD43"], main = "After gating")

par(mfrow=c(1,1))

JhuangLab/CytoTree documentation built on Nov. 16, 2020, 7:23 a.m.