flowFlowJo-package        package:flowFlowJo        R Documentation

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_D_e_s_c_r_i_p_t_i_o_n:

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

_D_e_t_a_i_l_s:


       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.

_N_o_t_e:

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

_A_u_t_h_o_r(_s):

     John Gosink <gosinkj@amgen.com>

_E_x_a_m_p_l_e_s:

     # 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.

