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)

