split_in_two-methods: Split an object in a low density region

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

Description

This method finds a split in the low density region of 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 left or righ (i.e, lower or higher) than density peak. An FCS channel shall be specified if a flowFrame object with multiple channels in provided on the input. If matrix is the input then it shall contain one column only. This method is designed to work well for 2 level beads, such as stained and unstained, but will not provide meaningful results for multi-level beads or other data in general.

Usage

    split_in_two(object, ...)

Arguments

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

Details

Additional parameter of the method:

channel

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

Value

A vector of TRUE/FALSE values depending on whether each of the events (rows) are below or above the identified split value.

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)
    ## Note that this is just to demonstrate the syntax, but doing this on the
    ## FSC and SSC channels of this particular FCS file is not very meaningful
    r1 <- split_in_two(myFlowFrame, 'FSC-H')
    r2 <- split_in_two(exprs(myFlowFrame[,'SSC-H']))

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