read.gatingML: Function to parse a Gating-ML XML file into objects in the R environment

Description

This function parses a Gating-ML XML file defined in compliance with the Gating-ML 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

Gating-ML XML file describing gates, transformations and/or compensations

flowEnv

environment into which the R objects created from the Gating-ML 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 Gating-ML versions 1.5 and 2.0 of the specification. Version 2.0 is the most recent at the time of this writing.

References

Spidlen J, ISAC DSTF, Brinkman RR. 2014. Gating-ML 2.0. International Society for Advancement of Cytometry (ISAC) standard for representing gating descriptions in flow cytometry. http://flowcyt.sf.net/gating/20141009.pdf http://flowcyt.sf.net/gating/20141009.full.zip

Spidlen J, Leif RC, Moore W, Roederer M, ISAC DSTF, Brinkman RR. 2008. Gating-ML: XML-based gating descriptions in flow cytometry. Cytometry A. 2008 Dec; 73A(12):1151--7. doi: 10.1002/cyto.a.20637.

Spidlen J, ISAC DSTF, Brinkman RR. 2008. Gating-ML Candidate Recommendation for Gating Description in Flow Cytometry version 1.5. http://flowcyt.sf.net/gating/Gating-ML.v1.5.081030.pdf http://flowcyt.sf.net/gating/Gating-ML.v1.5.081030.full.zip http://flowcyt.sf.net/gating/Gating-ML.v1.5.081030.Compliance-tests.081030.zip

Examples

Run this code

library("flowCore")

#########################
# Gating-ML 2.0 example #
#########################
flowEnv <- new.env()

fcsFile <- system.file("extdata/Gml2/FCSFiles", 
  "data1.fcs", package="gatingMLData")
fcs <- read.FCS(fcsFile, 
  transformation="linearize-with-PnG-scaling")

gateFile <- system.file("extdata/Gml2/Gating-MLFiles", 
  "gates1.xml", package="gatingMLData")
read.gatingML(gateFile, flowEnv)
ls(flowEnv)

result = filter(fcs, flowEnv$Polygon1)
summary(result)

#########################
# Gating-ML 1.5 example #
#########################
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)

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