timeFilter-class: Class "timeFilter"

In RGLab/flowCore: flowCore: Basic structures for flow cytometry data

Class "timeFilter"

Description

Define a filter that removes stretches of unusual data distribution within a single parameter over time. This can be used to correct for problems during data acquisition like air bubbles or clods.

Usage

timeFilter(..., bandwidth=0.75, binSize, timeParameter,
filterId="defaultTimeFilter")

Arguments

...	The names of the parameters on which the filter is supposed to work on. Names can either be given as individual arguments, or as a list or a character vector.
filterId	An optional parameter that sets the filterId slot of this gate. The object can later be identified by this name.
bandwidth, binSize	Numerics used to set the bandwidth and binSize slots of the object.
timeParameter	Character used to set the timeParameter slot of the object.

Details

Clods and disturbances in the laminar flow of a FACS instrument can cause temporal aberrations in the data acquisition that lead to artifactual values. timeFilters try to identify such stretches of disturbance by computing local variance and location estimates and to remove them from the data.

Value

Returns a timeFilter object for use in filtering flowFrames or other flow cytometry objects.

Slots

bandwidth

Object of class "numeric". The sensitivity of the filter, i.e., the amount of local variance of the signal we want to allow.

binSize

Object of class "numeric". The size of the bins used for the local variance and location estimation. If NULL, a reasonable default is used when evaluating the filter.

timeParameter

Object of class "character", used to define the time domain parameter. If NULL, the filter tries to guess the time domain from the flowFrame.

parameters

Object of class "character", describing the parameters used to filter the flowFrame.

filterId

Object of class "character", referencing the filter.

Extends

Class "parameterFilter", directly.

Class "concreteFilter", by class parameterFilter, distance 2.

Class "filter", by class parameterFilter, distance 3.

Objects from the Class

Objects can be created by calls of the form new("timeFilter", ...) or using the constructor timeFilter. Using the constructor is the recommended way.

Methods

%in%

signature(x = "flowFrame", table = "timeFilter"): The workhorse used to evaluate the filter on data. This is usually not called directly by the user.

show

signature(object = "timeFilter"): Print information about the filter.

Note

See the documentation of timeLinePlot in the flowViz package for details on visualizing temporal problems in flow cytometry data.

Author(s)

Florian Hahne

See Also

flowFrame, filter for evaluation of timeFilters and split and Subsetfor splitting and subsetting of flow cytometry data sets based on that.

Examples

## Loading example data
data(GvHD)
dat <- GvHD[1:10]

## create the filter
tf <- timeFilter("SSC-H", bandwidth=1, filterId="myTimeFilter")
tf

## Visualize problems
## Not run: 
library(flowViz)
timeLinePlot(dat, "SSC-H")

## End(Not run)

## Filtering using timeFilters
fres <- filter(dat, tf)
fres[[1]]
summary(fres[[1]])
summary(fres[[7]])

## The result of rectangle filtering is a logical subset
cleanDat <- Subset(dat, fres)

## Visualizing after cleaning up
## Not run: 
timeLinePlot(cleanDat, "SSC-H")

## End(Not run)

## We can also split, in which case we get those events in and those
## not in the gate as separate populations
allDat <- split(dat[[7]], fres[[7]])

par(mfcol=c(1,3))
plot(exprs(dat[[7]])[, "SSC-H"], pch=".")
plot(exprs(cleanDat[[7]])[, "SSC-H"], pch=".")
plot(exprs(allDat[[2]])[, "SSC-H"], pch=".")

RGLab/flowCore documentation built on Aug. 26, 2024, 8:52 a.m.