getTopTable             package:cellHTS2             R Documentation

_G_e_n_e_r_a_t_e _t_h_e _h_i_t _l_i_s_t _f_r_o_m _a _s_c_o_r_e_d _c_e_l_l_H_T_S _o_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     Generate the hit list from a scored 'cellHTS' object and write it
     to a tab-delimited file.

_U_s_a_g_e:

     getTopTable(cellHTSlist, file="topTable.txt", verbose=interactive())

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

cellHTSlist: a list of 'cellHTS' objects. See details.

    file: the name of the output file. Default is "topTable.txt".

 verbose: a logical value, if 'TRUE', the function reports its
          progress. Defaults to the state of 'interactive()'.

_D_e_t_a_i_l_s:

     Argument 'cellHTSlist' should be a list containing at least one
     component named "scored" which corresponds to a scored 'cellHTS'
     object. Other possible components of 'cellHTSlist' can be:



     '"_r_a_w"': a 'cellHTS' object containing unpreprocessed data. I.e.
          'state(cellHTSlist[["raw"]])["normalized"]=FALSE'.

     '"_n_o_r_m_a_l_i_z_e_d"': a 'cellHTS' object containing normalized data.
          I.e. 'state(cellHTSlist[["normalized"]])["normalized"]=TRUE'
          and 'state(cellHTSlist[["normalized"]])["scored"]=FALSE'.


     All of the components of 'cellHTSlist' should be 'cellHTS' objects
     containing data from the same experiment, but in different
     preprocessing stages.

     This function generates a 'data.frame' that is written to 'file'. 
     This data.frame and the output file contain the list of scored
     probes ordered by decreasing score values. They have one row for
     each well and plate, and contain the following columns (depending
     on the components of 'cellHTSlist'):



     '_p_l_a_t_e': plate identifier for each well.

     '_p_o_s_i_t_i_o_n': gives the position of the well in the plate (ranges
          from 1 to the total number of wells in the plate).

     '_w_e_l_l': gives the alphanumeric identifier for the wells.

     '_s_c_o_r_e': content of slot 'assayData' of the scored 'cellHTS'
          object given in 'cellHTSlist[["scored"]]'.

     _c_o_d_e{_w_e_l_l_A_n_n_o}: ell annotation as given by the plate configuration
          file.

     _c_o_d_e{_f_i_n_a_l_W_e_l_l_A_n_n_o}: gives the final well annotation for the
          scored values.  It combines the information given in the
          plate configuration file with the values in 'assayData' slot
          of the scored 'cellHTS' object, in order to have into account
          the wells that have been flagged either by the screen log
          file, or manually by the user during the analysis. These
          flagged wells appear with the annotation _flagged_.

     '_r_a_w__r_i__c_h_j': (if 'cellHTSlist[["raw"]]' is given) contains the
          raw intensities for replicate 'i' in channel 'j' (content of
          slot 'assayData' of the 'cellHTS' object given in
          'cellHTSlist[["raw"]]').

     '_m_e_d_i_a_n__c_h_j': (if 'cellHTSlist[["raw"]]' is given) corresponds to
          the median of raw measurements across replicates in channel
          'j'.

     '_d_i_f_f__c_h_j': (if 'cellHTSlist[["raw"]]' is given and if there are
          two replicates or samples) gives the difference between
          replicate (sample) raw measurements in channel 'j'.

     '_a_v_e_r_a_g_e__c_h_j': (if 'cellHTSlist[["raw"]]' is given and if there
          are more than 2 replicates or samples) corresponds to the
          average between replicate raw intensities for channel 'j'.

     '_r_a_w/_P_l_a_t_e_M_e_d_i_a_n__r_i__c_h_j': (if 'cellHTSlist[["raw"]]' is given)
          this column gives the ratio between each raw measurement and
          the median intensity in each plate for replicate (or sample)
          'i' in channel 'j'. The plate median is determined for the
          raw intensities using exclusively the wells annotated as
          'sample'.

     '_n_o_r_m_a_l_i_z_e_d__r_i__c_h_j': (if 'cellHTSlist[["normalized"]]' is given)
          gives the normalized intensities for replicate (sample) 'i'
          in channel 'j'. This corresponds to the content of slot
          'assayData' of the 'cellHTS' object given in
          'cellHTSlist[["normalized"]]'.


     Additionally, if the 'cellHTS' object given in
     'cellHTSlist[["scored"]]' is already annotated, the output
     'topTable' also contains the gene annotation stored in slot
     'featureData'.

_V_a_l_u_e:

     Generates the file with the hit list and outputs a 'data.frame'
     with the same contents.

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

     Ligia P. 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:

     'cellHTS'

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

         data(KcViabSmall)
         xn <- normalizePlates(KcViabSmall, scale="multiplicative", log=FALSE, method="median", varianceAdjust="none") 
         xsc <- scoreReplicates(xn, sign="-", method="zscore")
         xsc <- summarizeReplicates(xsc, summary="mean")
         out <- getTopTable(cellHTSlist=list("raw"=KcViabSmall, "normalized"=xn, "scored"=xsc), file=tempfile())

