removeLowDensSections: Remove low density regions of a flowFrame.

In jmeskas/flowCut: Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis

Remove low density regions of a flowFrame.

Description

Remove low density regions of a flowFrame.

Usage

    removeLowDensSections (f, Time.loc, Segment=500, LowDensityRemoval=0.1, Verbose=FALSE)

Arguments

f	A single flowFrame to be processed.
Time.loc	An positive interger value for the location of the time channel.
Segment	An integer value that specifies the number of events in each segment to be analyzed. A single segment is defaulted to contain 500 events.
LowDensityRemoval	An numeric value between 0 and 1 that specifies the proportion cut-off of the low density region. All events with less density than LowDensityRemoval will be removed. The default is 0.1.
Verbose	A logical value that dictates if computational information is printed while the code is running. The default is FALSE.

Details

removeLowDensSections removes low density regions of a flowFlame. The flowFrame must have a time channel.

Value

A list containing two elements. The first element, $frame, is the flowFrame file returned after removeLowDensSections has removed the low density sections. The second element, $rem.ind, is a vector containing indices of events being removed.

Author(s)

Maintainer: Justin Meskas [e-mail], Sherrie Wang [e-mail]

Examples

data(flowCutData)
res_lowDens <- removeLowDensSections(flowCutData[[1]], LowDensityRemoval=0.1, Time.loc=which(parameters(flowCutData[[1]])$name == "Time"))
library(flowDensity)
plotDens(flowCutData[[1]], c("Time","FL1-H"))
points(exprs(flowCutData[[1]])[res_lowDens$rem.ind, c("Time","FL1-H")],
    pch=".", col="grey")

jmeskas/flowCut documentation built on March 31, 2022, 11:04 a.m.