incorporatepValVec         package:RNAither         R Documentation

_I_n_c_o_r_p_o_r_a_t_e _a _v_e_c_t_o_r _o_f _p-_v_a_l_u_e_s _i_n_t_o _a _d_a_t_a_s_e_t

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

     Incorporates a vector of p-values into a dataset. Also works with
     a dataset containing values per well (non summarized), or with a
     hit vector.

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

     incorporatepValVec(dataset, pValVec, replicaMatrix, col4anno, colname4pval)

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

 dataset: an R data frame generated with 'generateDatasetFile' 

 pValVec: a vector of p-values 

replicaMatrix: a matrix of replicate values, as generated by
          'generateReplicateMat' 

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

colname4pval: a character string specifying the name of the dataset
          column the p-values will be stored in 

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

     Returns the dataset with an added column of p-values.

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

     'multTestAdjust', 'Ttest'

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

     data(exampleDataset, package="RNAither")

     data(scoredDataset1, package="RNAither")
     ##scoredDataset1 already contains the p-value column
     data(pValVec1, package="RNAither")

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

     temp <- generateReplicateMat(dataset, 1, "Intensities", "SigIntensity",  "GeneName")
     replicamatrix <- temp[[1]]
     newdataset <- incorporatepValVec(dataset, pValVec1, replicamatrix, "GeneName", "pvals")
     ##newdataset and scoredDataset1 are now equivalent

