simplifyGateNames         package:flowFlowJo         R Documentation

_S_t_a_n_d_a_r_d_i_z_e _f_l_o_w _c_y_t_o_m_e_t_r_y _g_a_t_e _n_a_m_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function helps to standardize typical flow cytometry cell
     population names. This is useful when trying to combine the
     results from a large number of flow runs wherein the cytometrist
     may have used slightly different nomenclature to describe the same
     set of cells.   For example, "Lymphocytes" vs. "lymphoctes".

_U_s_a_g_e:

      
     simplifyGateNames(x, ...) 

_A_r_g_u_m_e_n_t_s:

       x: Logical.  Default=FALSE.  A flowCore style filter, or a text
          string with a gate (filter) name 

     ...: Additional arguments:     _upperCaseGates_ Logical. 
          Default=FALSE.  If TRUE, convert the gate names to all upper
          case    
           _stripFileName_  Logical.  Default=TRUE.  It is currently
          the convention that the flowFlowJo code prepends the name of
          the referenced FCS file within the gate name, followed by a
          colon, then the rest of the gate information.  This setting
          looks for ".*\.fcs:" and strips it out of the gate name   
            _removeParentalNames_ Logical.  Default=TRUE.  The current
          _getFlowJoGates_ method concatenates a gate's name with the
          name of all of it's parents.  


_V_a_l_u_e:

     This function returns either a text string or flowCore style
     filter object.

_A_u_t_h_o_r(_s):

     John Gosink

_E_x_a_m_p_l_e_s:

      
     simplifyGateNames(c("LymphoCytes", "lymphocytes", "mOnOcYtEs"));
     simplifyGateNames(c("Lymphocytes:CD8+"), removeParentalNames=TRUE); 
     simplifyGateNames("CD34 positive cells ") 
     simplifyGateNames("CD34 + ") 

