summarizeReplicates        package:maigesPack        R Documentation

_S_u_m_m_a_r_i_s_e _m_i_c_r_o_a_r_r_a_y _o_b_j_e_c_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Function to summarise measures of a 'maiges' class object, both by
     samples and genes.

_U_s_a_g_e:

     summarizeReplicates(object=NULL, gLabelID="GeneName", sLabelID="Sample",
                         funcS="mean", funcG="mean", rmBad=TRUE, keepEmpty=TRUE)

_A_r_g_u_m_e_n_t_s:

  object: object of class 'maiges'.

gLabelID: character string giving the gene label ID to be used to
          summarise the data by rows.

sLabelID: character string giving the sample label ID to be used to
          summarise the data by columns.

   funcS: character string specifying the function to be applied for
          sample replicates. Defaults to 'mean'. If NULL, no resume is
          done for samples.

   funcG: character string specifying the function to be applied for
          genes (spots) replicates. Defaults to 'mean'. If NULL, no
          resume is done for genes..

   rmBad: logical indicating if you want to remove or not bad spots,
          given by the slot 'BadSpots' in argument 'object'.

keepEmpty: logical indicating if you want to maintain spots with empty
          information.

_D_e_t_a_i_l_s:

     This function takes the object of class 'maiges' and resume the
     data by spots (rows) and samples (columns).

_V_a_l_u_e:

     This function returns another object of class 'maiges' with
     replicates summarised to only one observation.

_A_u_t_h_o_r(_s):

     Gustavo H. Esteves <gesteves@vision.ime.usp.br>

_E_x_a_m_p_l_e_s:

     ## Loading the dataset
     data(gastro)

     ## Summarising the data (maigesNorm class), replicated samples will be
     ## summarised by mean and genes by median
     gastro.summ = summarizeReplicates(gastro.norm, gLabelID="GeneName",
       sLabelID="Sample", funcS="mean", funcG="median",
       keepEmpty=FALSE, rmBad=FALSE)

     ## To summarise genes by mean and keep the blank spots use
     gastro.summ = summarizeReplicates(gastro.norm, gLabelID="GeneName",
       sLabelID="Sample", funcS="mean", funcG="mean",
       keepEmpty=TRUE, rmBad=FALSE)

