collectSummaryFlowInfo      package:flowFlowJo      R Documentation

_C_o_l_l_e_c_t _P_o_p_u_l_a_t_i_o_n _S_t_a_t_i_s_t_i_c_s _o_n _F_l_o_w _F_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Creates a data structure containing a comprehensive list of
     summary statistics and related information on the cell populations
     of the FCS files referenced in one or more FlowJo workspaces.

_U_s_a_g_e:

       
     collectSummaryFlowInfo(fj, ...)  

_A_r_g_u_m_e_n_t_s:

      fj: a flowJoList object.  See readFlowJoList. 

     ...: Additional arguments detailed below:  

_D_e_t_a_i_l_s:

     Additional arguments also include the following:  


        fileNamePatterns - a vector of patterns that will be used to
     pick only specific FCS files from amongst all the FCS files listed
     in FlowJo workspaces.  The default (\dQuote{.}) returns all of
     them.  
        gateNamePattern  - a vector of patterns that will be used to
     pick only a subset of all the gates for all FCS files listed in
     the FlowJo workspaces.  The default (\dQuote{.}) returns all of
     them.  \emph{Not implemented yet.}  
        upperCaseGates   - Logical.  Default = FALSE.  If TRUE,
     converts all gate names to upper case.    
        keywords         - a vector of fields that you want to retrieve
     from the text section of each FCS file.   
        stripGutters     - Logical.  Currently FALSE and
     non-functional.  Whether or not to strip out gutter events before
     doing the main gating.   
        method           - what type of measurement to use for MFIs on
     each population.  One of mean, median (default), or mode. 
     \emph{Only median is currently implemented.}   


_V_a_l_u_e:

     The method collectSummaryFlowInfo returns a moderately complex
     data structure called an _fcsSummaryList_ detailing summary
     statistics and other information from the cell populations listed
     in one or more FlowJo workspaces.  The main argument for this
     method is a flowJoList object that was created using the
     readFlowJoList method.  The key issue here is that parsing a set
     of FlowJo workspaces and converting the referenced gates into
     flowCore style filters takes only a few seconds or minutes. 
     Reading in each of the referenced FCS files in a very large
     experiment and gating them with the filters (which this code
     does), may take many hours.  Thus this method also includes two
     arguments  (_fileNamePatterns_ and _gateNamePatterns_) to reduce
     the number of FCS files examined.  This method may, optionally,
     search the text/header section of each FCS file looking for
     specific keywords (e.g. $P2R, or $DATE, etc.) and collect the
     appropriate values.  Finally, one of the main operations of this
     method is to collect the MFIs cell counts for each population in
     each FCS file.  The user can choose either mean, median, or mode
     for the MFI values.  Returned values are in untransformed units
     (e.g. not log intensities).

_A_u_t_h_o_r(_s):

     John Gosink

_R_e_f_e_r_e_n_c_e_s:

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

_E_x_a_m_p_l_e_s:

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

     # This next statement may take a few moments to run as it is parsing through a FlowJo workspace
     # and two dozen FCS files...
     summaryStatsObj <- collectSummaryFlowInfo(testList);

