generateReplicateMat        package:RNAither        R Documentation

_G_e_n_e_r_a_t_e _a _m_a_t_r_i_x _o_f _r_e_p_l_i_c_a_t_e_s

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

     Generates a matrix out of a dataset, each row corresponding to an
     siRNA/gene ID, each column to a channel value or its index in the
     dataset.

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

     generateReplicateMat(data, minNbReps, IndexOrInt, col4val, col4anno)

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

    data: an R data frame generated with 'generateDatasetFile' 

minNbReps: set to 2 if you want to exclude replicates occurring only
          once in the dataset, otherwise 1. 

IndexOrInt: a character string - either ' "Index"' or ' "Intensities"'
          - specifying which values are to be contained in the output
          matrix. 

 col4val: a character string specifying the name of the dataset column
          to be used for the values of the output matrix (if '
          IndexOrIntensities' is set to ' "Intensities"'), for example
          ' "SigIntensity"' or ' "NbCells"' 

col4anno: a character string specifying the name of the dataset column
          to be used for the output matrix' rows, for example '
          "GeneName"' or ' "Internal_GeneID"'. 

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

     The function will omit values or indexes of lines/wells whose
     value in the column specified by ' colname4val' is set to NA,
     (which is the case if the spot type is set to -1). If you do not
     want to omit those, use 'generateRepMatNoFilter'.

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

     A matrix with each row corresponding to an siRNA/gene ID (as
     reflected in rownames), each column to a channel value or its
     index in the dataset. Missing values (in case of different number
     of replicates occuring for different siRNAs/genes) are set to NA.

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

     'generateRepMatNoFilter'

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

     data(exampleDataset, package="RNAither")

     replicatematrix <- generateReplicateMat(dataset, 2, "Index", "SigIntensity",  "GeneName")

