transform: tranform the flow data asssociated with the GatingSet

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

tranform the flow data asssociated with the GatingSet

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)

RGLab/flowWorkspace documentation built on March 17, 2024, 2:24 p.m.