flowFlowJo-package: Turn FlowJo workspaces into flowCore compliant objects

In flowFlowJo: Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm.

Description

Extract information, gates, FCS file (locations) etc. from a FlowJo workspace

Details

Package:	flowFlowJo
Type:	Package
Version:	1.16
Date:	2008-09-25
License:	GPL 3 or newer

FlowJo is a commercially available software package used in gating and analyzing data from flow cytometry experiments. Upon saving, FlowJo produces an XML format file that contains all the information necessary to describe the gating structures, compensation, transformation, location of the FCS files, and opened graphs and figures last created by the user. This package (flowFlowJo) is a small set of methods designed to extract the file locations, gates, compensation matrices and other meta-data contained in FlowJo workspaces and return the information in a manner consistent with the BioConductor flowCore packages.

Note

See a complete discussion with examples via: vignette("flowFlowJo")

Author(s)

John Gosink <[e-mail]>

Examples

# A demo set of FCS files and attendant FlowJo workspace are included with
# this package.  This extracts the info from the workspace.

library(flowFlowJo);
demoLocation <- system.file("extdata", "DemoWorkspace.wsp", package="flowFlowJo"); 
actualFCSLoc <- system.file("extdata/fcsFiles", package="flowFlowJo"); 
testList     <- readFlowJoList(demoLocation, altFileLocation=actualFCSLoc);
z            <- getFlowJoGates(testList, fileNamePatterns=c("C02"));

# Take a look at z.  It contains the name(s), location(s), compensation matrix, gate/filter(s) 
# and gate/filter names for one of the FCS files referenced in the workspace.

flowFlowJo documentation built on Sept. 12, 2016, 6:14 a.m.