hitselectionPval          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 _p-_v_a_l_u_e_s

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

     Selects significant genes according to their p-value.

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

     hitselectionPval(dataset, pValVec, col4val, col4sel, thresh, col4anno, 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' 

 col4val: a character vector specifying a column of intensity values 

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

  thresh: the threshold for the p-values, typically 0.05 

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

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 'thresh', the
     threshold is increased to 'min(pvalvec)'.

_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

replicaMatrix : a matrix of replicates with corresponding values (as
          generated by 'generateReplicateMat')

 thresh : the threshold for the p-values

     P-values and the intensity values for each siRNA are stored in a
     text output file.

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

     'hitselectionZscore', '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 <- hitselectionPval(scoredDataset1, pValVec1, "SigIntensity", "Pval_hits", 0.05, 
     "GeneName", "pvalue_testfile1.txt")

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

