read.gatingML {flowUtils} | R Documentation |
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.
read.gatingML(file,flowEnv,...)
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 |
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.
Gopalakrishnan N
Gating-ML Candidate Recommendation for Gating Description in Flow Cytometry V 1.5
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)