timeFilter-class {flowCore} | R Documentation |
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.
timeFilter(..., bandwidth=0.75, binSize, timeParameter, filterId="defaultTimeFilter")
... |
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 |
bandwidth, binSize |
Numerics used to set the |
timeParameter |
Character used to set the |
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.
Returns a timeFilter object for use in filtering
flowFrame
s or other flow cytometry objects.
Class "parameterFilter"
, directly.
Class "concreteFilter"
, by class
parameterFilter
, distance 2.
Class "filter"
, by class parameterFilter
,
distance 3.
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.
Objects can be created by calls of the form new("timeFilter",
...)
or using the constructor timeFilter
. Using the
constructor is the recommended way of object instantiation:
signature(x = "flowFrame", table =
"timeFilter")
: The workhorse used to evaluate the filter on
data. This is usually not called directly by the user.
signature(object = "timeFilter")
: Print
information about the filter.
See the documentation of
timeLinePlot
in the
flowViz
package for details on
visualizing temporal problems in flow cytometry data.
Florian Hahne
flowFrame
, filter
for
evaluation of timeFilters
and split
and
Subset
for splitting and subsetting of flow cytometry
data sets based on that.
## 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=".")