read.gatingML {flowUtils}R Documentation

Function to parse an XML gating File into objects in the R enviroment

Description

This function parses an XML file defined in compliance with the Gating-ML candidate recommendation into objects in the R environment, which can then be evaluated using functions provided by the flowCore package.

Usage

read.gatingML(file,flowEnv,...)

Arguments

file XML file describing gates,transformations or compensations
flowEnv environment into which the R objects created from the XML file are to be stored
... additional arguments that are passed to the methods

Details

The Gating-ML specification has been developed as an interchange format for the description of gates relevant to a flow cytometry experiment. Presently, we can read version 1.5 of the specification, which was the most recent at the time of this writing.

Author(s)

Gopalakrishnan N

References

Gating-ML Candidate Recommendation for Gating Description in Flow Cytometry V 1.5

Examples


 flowEnv=new.env()

 fcsFile<-system.file("extdata/List-modeDataFiles","fcs2_int16_13367ev_8par_GvHD.fcs",package="gatingMLData")
 fcs <- read.FCS(fcsFile,transformation=FALSE)
 
 gateFile <- system.file("extdata/Gating-MLFiles","02CtSRectangular.xml",package="gatingMLData")
 read.gatingML(gateFile,flowEnv)
 
 ls(flowEnv)
  
 result=filter(fcs,flowEnv$CtSR_03)
 summary(result)

[Package flowUtils version 1.2.0 Index]