Subset: Subset a flowFrame or a flowSet

Description

An equivalent of a subset function for flowFrame or a flowSet object. Alternatively, the regular subsetting operators can be used for most of the topics documented here.

Usage

Subset(x, subset, ...)

Arguments

The flow object, frame or set, to subset.

subset

A filter object or, in the case of flowSet subsetting, a named list of filters.

...

Like the original subset function, you can also select columns.

Value

Depending on the original context, either a flowFrame or a flowSet.

Details

The Subset method is the recommended method for obtaining a flowFrame that only contains events consistent with a particular filter. It is functionally equivalent to frame[as(filter(frame,subset),"logical"),] when used in the flowFrame context. Used in the flowSet context, it is equivalent to using fsApply to apply the filtering operation to each flowFrame.

Additionally, using Subset on a flowSet can also take a named list as the subset. In this case, the names of the list object should correspond to the sampleNames of the flowSet, allowing a different filter to be applied to each frame. If not all of the names are used or excess names are present, a warning will be generated but the valid filters will be applied for the rare instances where this is the intended operation. Note that a filter operation will generate a list of filterResult objects that can be used directly with Subset in this manner.

Examples

Run this code


sample <- read.flowSet(path=system.file("extdata", package="flowCore"),
pattern="0877408774")
result <- filter(sample, rectangleGate("FSC-H"=c(-Inf, 1024)))
result
Subset(sample,result)

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