flowFlowJo-package        package:flowFlowJo        R Documentation

_T_u_r_n _F_l_o_w_J_o _w_o_r_k_s_p_a_c_e_s _i_n_t_o _f_l_o_w_C_o_r_e _c_o_m_p_l_i_a_n_t _o_b_j_e_c_t_s

_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.

