getFlowJoGates          package:flowFlowJo          R Documentation

_g_e_t_F_l_o_w_J_o_G_a_t_e_s

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

     Given a parsed FlowJo workspace (flowJoObj) or list of FlowJo
     workspaces (flowJoList), return an indexed list of the gates, as
     flowCore style filter objects, for each of the FCS files.  Also
     get the associated compensation matrices.

_U_s_a_g_e:

     getFlowJoGates(fj, fileNamePatterns)

_A_r_g_u_m_e_n_t_s:

      fj: a flowJoList or flowJoObj 

fileNamePatterns: a vector of one or more patterns used to pick
          specific FCS files from the complete list of FCS files (with
          their paths) listed in the FlowJo workspace(s).  The default
          is . - ie all of the FCS files will be chosen. 

_V_a_l_u_e:

     The method getFlowJoGates returns a list of ordered lists which
     includes references to a set of FCS files, their locations, all
     gating structures related to them (as flowCore filter objects),
     the names of those gates (filters), and the associated
     compensation matrices for the FCS files.

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

     John Gosink

_S_e_e _A_l_s_o:

     See also FlowJo from TreeStar Inc, at:  <URL:
     http://www.flowjo.com/>

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

     # Note this may take a moment to process the whole XML file
     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("A01"));

