hitselectionZscorePval       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 _a_n_d _p-_v_a_l_u_e_s

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

     Selects significant genes according to their ZScore (summarized
     with the gene median) and p-values.

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

     hitselectionZscorePval(dataset, pValVec, col4zscore, col4sel, thresh, thresh2, 
     flag2, col4anno, sumFunc, file4hits)

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

 dataset: an R data frame generated with 'generateDatasetFile' 

 pValVec: a vector of p-values, as generated by one of the test
          functions 'Ttest', 'MannWhitney' or 'RankProduct' 

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'. 

 thresh2: the threshold for the p-values 

   flag2: 2 or -2. 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 there are no p-values under the defined threshold ' thresh2',
     it is increased to ' min(pvalvec)'. 

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

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

     If there are not hits for the combined threshold of p-values and
     ZScores, the ZScore threshold is changed until there is a hit.

_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

thresh2 : he threshold for the p-values

     ZScores and p-values are stored in a text output file.

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

     'hitselectionPval', 'hitselectionZscore', '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 <- hitselectionZscorePval(scoredDataset1, pValVec1, "SigIntensity", 
     "Zscore_pval_hits", -1.5, 0.05, -2, "GeneName", median, "Zscores_pvals_testfile1.txt")

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

