annotate              package:cellHTS2              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:

     ## S4 method for signature 'cellHTS':
     annotate(object, geneIDFile, path)

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

  object: 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.

    path: a character of length 1 indicating the path in which to find
          the gene annotation file. By default,  it can extract the
          path from 'geneIDFile'.

_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 S4 object of class 'cellHTS', which inherits from class
     'NChannelSet'. The following slots are updates after calling this
     function: 

featureData: the contents of the annotation file are stored here.

   state: the processing status of the 'cellHTS' object is updated to
          'state["annotated"]= TRUE'.

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

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

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

     Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of
     cell-based RNAi screens, _Genome Biology_ *7*, R66.

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

     'readPlateList', 'configure'

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

         datadir <- system.file("KcViabSmall", package = "cellHTS2")
         x <- readPlateList("Platelist.txt", path=datadir, name="KcViabSmall")
         x <- configure(x, "Description.txt", "Plateconf.txt", "Screenlog.txt", path=datadir)
         x <- annotate(x, "GeneIDs_Dm_HFAsubset_1.1.txt", path=datadir)

