landmarkMatrix           package:flowStats           R Documentation

_C_o_m_p_u_t_e _a_n_d _c_l_u_s_t_e_r _h_i_g_h _d_e_n_s_i_t_y _r_e_g_i_o_n_s _i_n _1_D

_D_e_s_c_r_i_p_t_i_o_n:

     This functions first identifies high-density regions for each
     'flowFrame' in a 'flowSet' and subsequently tries to cluster these
     regions, yielding the landmarks matrix that needs to be supplied
     to 'landmarkreg'. The function is considered to be internal.

_U_s_a_g_e:

     landmarkMatrix(data, fres, parm, border=0.05, peakNr=NULL, densities = NULL, n = 201)

_A_r_g_u_m_e_n_t_s:

    data: A 'flowSet'. 

    fres: A list of 'filterResultList' objects generated by a filtering
          opration using a 'curv1Filter'. Each list item represents the
          results for one of the flow parameters in 'parm'.

    parm: Character scalar of flow paramater to compute landmarks for. 

  border: A numeric in '[0,1]'. Ignore all high-density regions with
          mean values in the extreme percentiles of the data range. 

  peakNr: Force a fixed number of peaks. 

densities: An optional matrix of y values of the density estimates for
          the 'flowSet'. If this is not present, density estimates will
          be calculated by the function. 

       n: Number of bins used for the density estimation. 

_D_e_t_a_i_l_s:

     In order to normalize the data using the 'landmarkreg' function in
     the 'fda', a set of landmarks has to be computed for each
     'flowFrame' in a 'flowSet'. The number of lansmarks has to be the
     same for each frame. This function identifies high-density regions
     in each frame, computes a simple clustering and returns a matrix
     of landmark locations. Missing landmarks of individual frames are
     substituted by the mean landmark location of the respective
     cluster.

_V_a_l_u_e:

     A matrix of landmark locations. Columns are landmarks and rows are
     'flowFrames'.

_A_u_t_h_o_r(_s):

     Florian Hahne

_S_e_e _A_l_s_o:

     'landmarkreg','warpSet'

_E_x_a_m_p_l_e_s:

     data(GvHD)
     tmp <- list("FSC-H"=filter(GvHD[1:3], curv1Filter("FSC-H")))
     res <-  flowStats:::landmarkMatrix(GvHD[1:3], tmp, "FSC-H")

