hitselectionZscore         package:RNAither         R Documentation

_S_e_l_e_c_t_i_n_g _h_i_t_s _a_c_c_o_r_d_i_n_g _t_o _Z_S_c_o_r_e_s

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

     Selects significant genes according to their ZScore.

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

     hitselectionZscore(dataset, col4zscore, col4sel, thresh, flag, flag2, col4anno, 
     sumFunc, file4hits)

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

 dataset: an R data frame generated with 'generateDatasetFile' 

col4zscore: a character vector specifying the name of the column
          containing the ZScores, usually 'SigIntensity' 

 col4sel: a character vector specifying the name of the new dataset
          column where hits will be stored 

  thresh: the threshold for the ZScores. The interpretation depends on
          the choice of the parameter ' flag2'. 

    flag: 1 or 2. 1 means the ZScores are kept per well, 2 that they
          are summarized according to the parameter ' sumFunc'. 

   flag2: 1, 2 or -2. 

          If 1 is chosen and ' thresh' == n, then the n greatest
          Zscores are chosen as hits. 

          If 1 is chosen and ' thresh' == -n, then the n smallest
          Zscores are chosen. 

          If 1 is chosen and ' thresh' == 0, all ZScores are chosen and
          written to the output file. 

          If 2 is chosen, all Zscores greater than or equal to '
          thresh' are chosen. 

          If -2 is chosen, all Zscores smaller than or equal to '
          thresh' are chosen.  

col4anno: a character string specifying the name of the dataset column
          to be used to define the replicate, for example ' "GeneName"'
          or ' "Internal_GeneID"' 

 sumFunc: the function used to summarize ZScore values, e.g. ' mean' or
          ' median'. 

file4hits: the name of the file to store the results in 

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

     If ' flag2' == -2, and there are no ZScores under the defined
     threshold ' thresh', the threshold is increased to '
     min(ZScores)'. 

     If ' flag2' == 2, and there are no ZScores over the defined
     threshold ' thresh', the threshold is increased to '
     max(ZScores)'.

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

     A list containing: 

dataset : the dataset with an added column defining the hits in the
          form of a binary vector

hitVector : the binary vector itself

 thresh : the threshold for the ZScores

     ZScores are stored in a text output file.

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

     N. Malo et al. Statistical practice in high-throughput screening
     data analysis. Nature Biotech, 24(2): 167-175, 2006.

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

     'hitselectionPval', 'hitselectionZscorePval', 'Ttest'

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

     data(scoredDataset1, package="RNAither")
     data(pValVec1, package="RNAither")

     ##for details on the generation of pValVec1 and scoredDataset1, see the example of the Ttest function linked above.

     scoredHits1 <- hitselectionZscore(scoredDataset1, "SigIntensity", "Zscore_hits", -10, 
     2, 1, "GeneName", median, "Zscores_testfile1.txt")

     newdataset <- scoredHits1[[1]]
     hitvector <- scoredHits1[[2]]

