transform: tranform the flow data asssociated with the GatingSet

In flowWorkspace: Infrastructure for representing and interacting with gated and ungated cytometry data sets.

Description

The transformation functions are saved in the GatingSet and can be retrieved by gh_get_transformations. Currently only flowJo-type biexponential transformation(either returned by gh_get_transformations or constructed by flowJoTrans) is supported.

Usage

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

Arguments

_data	GatingSet or GatingSetList
translist	expect a transformList object or a list of transformList objects(with names matched to sample names)
...	other arguments passed to 'transform' method for 'ncdfFlowSet'.(e.g. 'ncdfFile')

Value

a GatingSet or GatingSetList object with the underling flow data transformed.

Examples

## Not run: 
library(flowCore)
data(GvHD)
fs <- GvHD[1:2]
gs <- GatingSet(fs)

#construct biexponential transformation function
biexpTrans <- flowjo_biexp_trans(channelRange=4096, maxValue=262144, pos=4.5,neg=0, widthBasis=-10)

#make a transformList object
chnls <- c("FL1-H", "FL2-H")
transList <- transformerList(chnls, biexpTrans)

#add it to GatingSet
gs_trans <- transform(gs, transList)


## End(Not run)

flowWorkspace documentation built on Nov. 8, 2020, 8:08 p.m.