annotate              package:cellHTS2              R Documentation

_A_n_n_o_t_a_t_e_s _t_h_e _r_e_a_g_e_n_t_s (_p_r_o_b_e_s) _o_f _a _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 reagents (probes) of a 'cellHTS' object. In
     RNAi-screens, there is a often a 1:1 correspondence between
     reagents and intended target genes, hence in this software package
     the term gene ID is used as a synonym.

_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 in each plate.

    path: a character of length 1 indicating the path in which to find
          the gene annotation file (optional).

_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 is obtained by copying
     'object' and updating the following slots:

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)

