peak_gate-methods: Gate a 1D density peak in the provided object

In flowQB: Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations

Description

This method finds a density peak in the provided object (which shall be either a matrix or flowCore's flowFrame object) and returns a vector of TRUE/FALSE depending on whether each of the events (rows) are in the density peak. An FCS channel shall be specified if a flowFrame object with multiple channels in provided on the input.

Usage

    peak_gate(object, ...)

Arguments

object	Object of class flowFrame or a matrix.
...	Additional options, see the details section.

Details

Additional parameters of the method:

channel

Which FCS channel shall be used in order to look for the density peak? This is applicable if a flowFrame object with several channels is used on the input.

R

The radius to be used when finding the peak; R=1 by default.

Value

A vector of TRUE/FALSE values depending on whether each of the events (rows) are located in the identified density peak.

Author(s)

Wayne Moore, Faysal El Khettabi, Josef Spidlen

Examples

    library('flowCore')
    library('flowQBData')
    
    fcsFilePath <- system.file("extdata", "SSFF_LSRII", "Other_Tests",
        "933745.fcs", package="flowQBData")

    myFlowFrame <- read.FCS(fcsFilePath)
    r1 <- peak_gate(myFlowFrame, 'FSC-H')
    r2 <- peak_gate(exprs(myFlowFrame[,'SSC-H']))
    ## r3 will have more events than r2
    r3 <- peak_gate(exprs(myFlowFrame[,'SSC-H']), R=1.5)

flowQB documentation built on May 6, 2019, 3:05 a.m.