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:

        *  '"raw"': a 'cellHTS' object containing unpreprocessed data.
           I.e. 'state(cellHTSlist[["raw"]])["normalized"]=FALSE'.

        *  '"normalized"': 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'):


        *  'plate': plate identifier for each well.

        *  'position': gives the position of the well in the plate
           (ranges from 1 to the total  number of wells in the plate).

        *  'well': gives the alphanumeric identifier for the wells.

        *  'score': content of slot 'assayData' of the scored 'cellHTS'
           object given in 'cellHTSlist[["scored"]]'.

        *  'wellAnno': well annotation as given by the plate
           configuration file.

        *  'finalWellAnno': 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_.

        *  'raw_ri_chj': (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"]]').

        *  'median_chj': (if 'cellHTSlist[["raw"]]' is given)
           corresponds to the median of raw measurements across
           replicates in channel 'j'.

        *  'diff_chj': (if 'cellHTSlist[["raw"]]' is given and if there
           are two replicates or samples) gives the difference between
           replicate (sample) raw measurements in channel 'j'.

        *  'average_chj': (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'.

        *  'raw/PlateMedian_ri_chj': (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'.

        *  'normalized_ri_chj': (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())

