fitted_ellipse_gate: Fit and apply an ellipse gate

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

Description

Fit an ellipse (or ellipsoid) gate on the most dense region of the selected channels of a flowFrame object.

Usage

    fitted_ellipse_gate(object, channels, R=1)

Arguments

object	A flowFrame object that will be gated by an automatically fitted ellipse (or ellipsoid) gate.
channels	A vector if indices or short channel names (valued of the \$PnN keywords) of channels that shall be used to fit an ellipse (or ellipsoid) gate. Typically, these would be the indeces or names of the forward and scatter channels in the input flowFrame, which will then be gated by a 2D ellipse gate (since 2 channels were provided). A multidimensional ellipsoid gate is fitted analogically if more than 2 channels are provided. A 1D "ellipsoid" gate (i.e., a range gate) is applied if only a single channel is specified.
R	An additional scaling factor for the radii of the ellipse/ellipsoid gate.

Details

First, events with negative values in the specified channels are removed. Next, the find_peak function is called on log transformed values of each of the specified channels. The returned lower and upper boundaries of each of the channels are used to fit an ellipse/ellipsoid gate. The radii of this gate are scalled by the value of the provided R argument. A new flowFrame object with only those events in this gate is returned.

Value

A flowFrame object gated by an automatically fitted ellipse or ellipsoid gate created in the specified channels.

Author(s)

Wayne Moore, Faysal El Khettabi, Josef Spidlen

See Also

find_peak

Examples

    library('flowCore')
    library('flowQBData')
    
    fcsFilePath <- system.file("extdata", "SSFF_LSRII", "Other_Tests",
        "933745.fcs", package="flowQBData")
    myFlowFrame <- read.FCS(fcsFilePath)
    gatedFlowFrame <- fitted_ellipse_gate(myFlowFrame, c('FSC-H', 'SSC-H'))

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