betweenAlignment           package:flagme           R Documentation

_D_a_t_a _S_t_r_u_c_t_u_r_e _f_o_r "_b_e_t_w_e_e_n" _a_l_i_g_n_m_e_n_t _o_f _m_a_n_y _G_C_M_S _s_a_m_p_l_e_s

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

     This function creates a "between" alignment (i.e. comparing merged
     peaks)

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

     betweenAlignment(pD,cAList,pAList,impList,filterMin=3,gap=0.7,D=10,usePeaks=TRUE,df=30,verbose=TRUE)

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

      pD: a 'peaksDataset' object

  cAList: 'list' of 'clusterAlignment' objects, one for each
          experimental group

  pAList: 'list' of 'progressiveAlignment' objects, one for each
          experimental group

 impList: 'list' of imputation lists

filterMin: minimum number of peaks within a merged peak to be kept in
          the analysis

     gap: gap parameter

       D: retention time penalty parameter

usePeaks: logical, whether to use peaks (if 'TRUE') or the full 2D
          profile alignment (if 'FALSE')

      df: distance from diagonal to calculate similarity

 verbose: logical, whether to print information

_D_e_t_a_i_l_s:

     'betweenAlignment' objects gives the data structure which stores
     the result of an alignment across several "pseudo" datasets. 
     These pseudo datasets are constructed by merging the "within"
     alignments.

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

     'betweenAlignment' object

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

     Mark Robinson

_R_e_f_e_r_e_n_c_e_s:

     Mark D Robinson (2008).  Methods for the analysis of gas
     chromatography - mass spectrometry data _PhD dissertation_
     University of Melbourne.

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

     'multipleAlignment'

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

     require(gcspikelite)
     # see 'multipleAlignment'

