validTreetype              package:xps              R Documentation

_V_a_l_i_d_a_t_e _T_r_e_e _T_y_p_e

_D_e_s_c_r_i_p_t_i_o_n:

     Validate tree type for corresponding data type.

_U_s_a_g_e:

     validTreetype(treetype, datatype)

_A_r_g_u_m_e_n_t_s:

treetype: tree type.

datatype: data type.

_D_e_t_a_i_l_s:

     Every 'ROOT' tree has an extension, which describes the type of
     data stored in this tree. For example, 'TestA1.cel' is the tree
     name that stores the CEL-file data for 'TestA1.CEL'.

     Trees with 'datatype="scheme"' have the following extensions: 
      'scm': scheme tree containing (x,y)-coordinates and mask for
     UNIT_ID. 
      'idx': unit tree containing UnitName (i.e. probeset id),
     NumCells, NumAtoms, UnitType, for UNIT_ID. 
      'prb': probe tree containing probe sequences. 
      'ann': transcript annotation tree. 
      'anx': exon annotation tree; exon arrays only. 
      'anp': probeset annotation tree; exon arrays only. 
      'cxy': coordinate tree containing CLF-file information; exon
     arrays only. 
      'exn': exon tree; exon arrays only. 
      'pbs': probeset tree; exon arrays only. 

     Trees with 'datatype="rawdata"' have the following extensions: 
      'cel': data tree containing CEL-file data.

     Trees with 'datatype="preprocess"' have the following extensions: 
      'int': intensity tree containing background-corrected
     intensities. 
      'sbg': background tree containing MAS4 sector background levels. 
      'wbg': background tree containing MAS5 weighted sector background
     levels. 
      'rbg': background tree containing RMA background levels. 
      'gbg': background tree containing GC-content background levels. 
      'cmn': cell tree containing preprocessed intensities using
     algorithm 'mean'. 
      'cmd': cell tree containing preprocessed intensities using
     algorithm 'median'. 
      'clw': cell tree containing preprocessed intensities using
     algorithm 'lowess'. 
      'css': cell tree containing preprocessed intensities using
     algorithm 'supsmu'. 
      'cqu': cell tree containing preprocessed intensities using
     algorithm 'quantile'. 
      'dc5': detection tree containing MAS5 detection call and p-value. 
      'dab': detection tree containing DABG detection call and p-value. 
      'amn': expression tree containing expression levels computed with
     'arithmetic mean'. 
      'gmn': expression tree containing expression levels computed with
     'geometric mean'. 
      'wmn': expression tree containing expression levels computed with
     'weighted mean'. 
      'wdf': expression tree containing expression levels computed with
     'weighted difference'. 
      'adf': expression tree containing expression levels computed with
     'average difference'. 
      'tbw': expression tree containing expression levels computed with
     'tukey biweight'. 
      'mdp': expression tree containing expression levels computed with
     'median polish'. 

     Trees with 'datatype="normation"' have the following extensions: 
      'tmn': expression tree after normalization using algorithm
     'trimmed mean'. 
      'med': expression tree after normalization using algorithm
     'median'. 
      'ksm': expression tree after normalization using algorithm
     'kernel smoother'. 
      'low': expression tree after normalization using algorithm
     'lowess'. 
      'sup': expression tree after normalization using algorithm
     'supsmu'. 
      'qua': expression tree after normalization using algorithm
     'quantile'. 
      'mdp': expression tree after normalization using algorithm
     'median polish'.

_V_a_l_u_e:

     Returns the valid 'treetype', otherwise an error message is
     returned.

_N_o_t_e:

     Not all tree types are used in the current package.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'getDatatype', 'type2Exten'

_E_x_a_m_p_l_e_s:

     validTreetype("prb", "scheme")
     validTreetype("cel", "rawdata")
     validTreetype("tbw", "preprocess")

