aggregateExprs             package:PGSEA             R Documentation

_A_g_g_r_e_g_a_t_e _e_x_p_r_e_s_s_i_o_n _d_a_t_a

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

     This function removes duplicates row names from an expression set,
     summarizing them with a function of the users choice. The "absMax"
     function located in package "reb" we have found to be useful.

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

     aggregateExprs(x, package = "hgu133plus2", using = "ENTREZID", FUN, ...)

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

       x: expression data - matrix, eSet, or exprSet

 package: annotation package of expression data 

   using: format type that gene IDs are converted to  

     FUN: function by which to summarize duplicated values 

     ...: exra parameters passed on to FUN 

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

     A matrix of expression data with the rows aggregated to a unique
     format chosen by the user. The new identifiers of the returned
     matrix are those specified with the "using" argument. To see
     possible values, use the ls() command illustrated below in the
     examples.

_A_u_t_h_o_r(_s):

     Kyle Furge <kyle.furge@vai.org> and Karl Dykema
     <karl.dykema@vai.org>

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

             if (require(hgu95av2) & require(annaffy)) {
         library(annaffy)
                     data(aafExpr)
         class(exprs(aafExpr))
         exprs(aafExpr)[1:4, 1:4]

                             #list possible values for the "using" argument
                     ls(pos=which(search()=="package:hgu95av2"))
                     
                     convert <- aggregateExprs(exprs(aafExpr),"hgu95av2",FUN=mean,na.rm=TRUE)
               convert[1:4,1:4]
             }

