annotate               package:cellHTS               R Documentation

_A_n_n_o_t_a_t_e_s _t_h_e _g_e_n_e _I_D_s _o_f _a _g_i_v_e_n _c_e_l_l_H_T_S _o_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     Annotate the gene IDs of a given cellHTS object.

_U_s_a_g_e:

     annotate(x, ...)
     ## S3 method for class 'cellHTS':
     annotate(x, geneIDFile, ...)

_A_r_g_u_m_e_n_t_s:

       x: a cellHTS object.

geneIDFile: the name of the file with the gene IDs (see details). This
          argument is just passed on to the 'read.table' function, so
          any of the valid argument types for 'read.table' are valid
          here, too. Must contain one row for each well and each plate.

     ...: additional parameters - ignored.

_D_e_t_a_i_l_s:

_g_e_n_e_I_D_F_i_l_e This file is expected to be a tab-delimited file with at
     least three columns, and column names 'Plate', 'Well' and
     'GeneID'. The contents of 'Plate' are expected to be integer.
     Further columns are allowed.

_V_a_l_u_e:

     An S3 object of class 'cellHTS', which extends the argument 'x' by
     the following element: 

geneAnno: a data.frame containing what was read from input file
          'geneIDFile'.  The number of rows is equal to the product
          between the number of wells in each plate and the number of
          plates.


     Moreover, the processing status of the 'cellHTS' object is updated
     in the slot 'state' to 'state["annotated"]= TRUE'. There are
     methods 'print.cellHTS', 'configure.cellHTS' and
     'annotate.cellHTS'.

_A_u_t_h_o_r(_s):

     Wolfgang Huber huber@ebi.ac.uk, Ligia Braz ligia@ebi.ac.uk

_R_e_f_e_r_e_n_c_e_s:

     ..

_E_x_a_m_p_l_e_s:

      datadir = system.file("KcViabSmall", package = "cellHTS")
      x = readPlateData("Platelist.txt", "KcViabSmall", path=datadir)
      confFile = system.file("KcViabSmall", "Plateconf.txt", package="cellHTS")
      logFile  = system.file("KcViabSmall", "Screenlog.txt", package="cellHTS")
      descripFile  = system.file("KcViabSmall", "DESCRIPTION.txt", package="cellHTS")
      x = configure(x, confFile, logFile, descripFile)
      geneIDFile = system.file("KcViabSmall", "GeneIDs.txt", package="cellHTS")
      x = annotate(x, geneIDFile)

