transform: Transform a flowFrame or flowSet

In flowCore: flowCore: Basic structures for flow cytometry data

Description

Similar to the base transform method, this will transform the values of a flowFrame or flowSet object according to the transformations specified in one of two ways: 1. a [transformList][flowCore::transformList-class] or list of [transform][flowCore::transform-class] objects 2. named arguments specifying transformations to be applied to channels (see details)

Usage

## S4 method for signature 'flowFrame'
transform(`_data`, translist, ...)

Arguments

_data	a flowFrame or flowSet object
translist	a transformList object
...	other arguments. e.g. 'FL1-H' = myFunc('FL1-H')

Details

To specify the transformations in the second way, the names of these arguments should correspond to the new channel names and the values should be functions applied to channels currently present in the flowFrame or flowSet. There are a few examples below.

Examples

data(GvHD)
# logarithmically transform FL1-H and FL2-H for the entire flowSet
# using a transformList
fs <- transform(GvHD,
                 transformList(c("FL1-H", "FL2-H"), list(log, log)))
                 
# transform a single flowFrame using named arguments. Note the first
# transformation will overwrite FL1-H while the second will create a new
# channel 
fr <- transform(GvHD[[1]],
                 `FL1-H`=log(`FL1-H`),
                 `logFL2`=log(`FL2-H`))

flowCore documentation built on Nov. 8, 2020, 5:19 p.m.