calc_mean_sd_capture: Calculate the mean and the standard deviation for the stained...

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

Description

This function calculates the mean and the standard deviation of two populations - one unstaned (low) and one stained (high) for a specified channel (specified by the value of the detector parameter). These populations are derived by first fitting an ellipse gate on the 2 specified scatter channels and then splitting for low and high based on the specified detector.

Usage

    calc_mean_sd_capture(fcs_file_path, scatter_channels, detector, dye)

Arguments

fcs_file_path	A character string specifying the file path to the FCS file with the acquired bead data.
scatter_channels	A vector of 2 short channel names (values of the $PnN keywords) specifying the 2 channels that should not be used to gate the main bead population. The first channel should be a forward scatter channel, the second one should be a side scatter channel.
detector	A character string specifying which channel to split for the low/high gate, which is also the channel that we calculate the mean and the standard deviation for.
dye	A character string specifying the desired column heading of the result.

Details

This function first fits an ellipse gate on the 2 specified scatter channels. This scatter gated population is then split to 2 (low=unstained and high=stained) in each of the fluorescence channels, and a peak gate is applied in order to isolate the high and the low peaks. Finally, the getOutliers method from the extremevalues package is used in order to calculate the mean and the standard deviation of both the stained and unstained population of each of the fluorescence channels. The value of the detector argument is used to determine which channel to work with, the value of the dye argument is only used to specify the column name of the result. These shall correspond to each other, e.g., "FITC-A" may be the value of the detector, which shall correspond to the short channel name of a channel in the FCS file. FITC may then be the desidered dye name, which will end be used for the column heading.

Value

The result is a data frame with a single column, the heading of the column corresponds to the value of the dye argument. The rows include the total number of events, the number of events in the FSC/SSC ellipse gate, the number of events in the high peak gate and low peak gate, the stained mean and stained standard deviation (based on the high peak gate), and finally the unstained mean and unstained standard deviation (based on the low peak gate).

Author(s)

Wayne Moore, Faysal El Khettabi, Josef Spidlen

See Also

calc_mean_sd_capture_all

Examples

    library(flowCore)
    library(flowQBData)

    fcs_file_path <- system.file("extdata", "SSFF_LSRII", "SU_2B",
        "933723.fcs", package="flowQBData")

    scatter_channels <- c("FSC-A", "SSC-A")
    detector <- "APC-A"
    dye <- "APC"
    
    results <- calc_mean_sd_capture(
        fcs_file_path, scatter_channels, detector, dye)

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