summarizeRepsNoFiltering      package:RNAither      R Documentation

_G_e_n_e_r_a_t_e _a _n_e_w _d_a_t_a_s_e_t _w_i_t_h _s_u_m_m_a_r_i_z_e_d _r_e_p_l_i_c_a_t_e_s

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

     Generates a new dataset with summarized replicates. Keeps
     wells/spots with 'SpotType' -1 in the dataset, but intensity
     values are replaced with 'NA'.

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

     summarizeRepsNoFiltering(data, funSum, col4val, col4anno, cols2del)

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

    data: an R data frame generated with 'generateDatasetFile' 

  funSum: a function used to summarize the values of a replicate, e.g.
          ' mean', ' median', 'rms', 'trim', ' max', ' min',
          'closestToZero', 'furthestFromZero', ... 

 col4val: a character vector (containing for example ' "SigIntensity"',
          ' Background', ' NbCells', ' PercCells', ...) specifying the
          columns that will be summarized by ' funSum' 

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

cols2del: a character vector containing the columns to delete, for
          example ' "SDSIntensity"' 

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

     All columns containing replicate values will be summarized by '
     funSum'. For all columns containing positions, screen numbers,
     plate numbers, etc., all information for different replicates will
     be kept, comma-separated. All columns containing standard
     deviations of channels should be specified in ' colnames2delete'.

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

     Returns the summarized dataset.

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

     'summarizeReps', 'eraseDataSetColumn', 'generateReplicateMat',
     'generateRepMatNoFilter', 'mean', 'median', 'rms', 'trim', 'max',
     'min', 'closestToZero', 'furthestFromZero'

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

     data(exampleDataset, package="RNAither")

     colname4val <- c("SigIntensity", "Background", "NbCells", "PercCells")
     summarizeddataset <- summarizeRepsNoFiltering(dataset, mean, colname4val, "GeneName", "SDSIntensity")

