filter {flowCore}R Documentation

Filter FCS files

Description

This function links filter descriptions to a particular set of flow cytometry data allowing for the lightweight calculation of summary statistics common to flow cytometry analysis.

Usage

filter(x,filter,...)

Arguments

x Object of class flowFrame or flowSet.
filter An object of class filter or a list of named filters.
... optional argument

Details

The filter method conceptually links a filter description, represented by a filter object, to a particular flowFrame. This is accomplished via the filterResult object, which tracks the linked flowFrame as well as caching the results of the filtering operation itself, allowing for fast calculation of certain summary statistics such as the percentage of events accepted by the filter. This method exists chiefly to allow the calculation of these statistics without the need to first Subset a flowFrame, which can be quite large.

Value

A filterResult object or a list of filterResult objects if x is a flowSet object. Note that filterResult objects are themselves filters, allowing them to be used in filter expressions or Subset operations.

Author(s)

N. Le Meur

See Also

filter-class, filterResult-class

Examples

 samp <- read.FCS(system.file("extdata","0877408774.B08", package="flowCore"))
 rectGate <- rectangleGate(filterId="nonDebris","FSC-H"=c(200,Inf))
 summary(filter(samp,rectGate))


[Package flowCore version 1.0.2 Index]