combineData               package:HELP               R Documentation

_C_o_m_b_i_n_e _d_a_t_a

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

     Calculate trimmed and/or weighted means of groups of rows in a
     given data matrix.

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

     combineData(x, y, w, ...)

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

       x: a numeric matrix containing the values whose trimmed and/or
          weighted mean is to be computed. Each column is treated
          independently. 

       y: a vector describing the discrete groups used to divide the
          elements of x.  If y is missing then all elements of x are
          handled together. 

       w: a matrix of weights the same dimensions as x giving the
          weights to use for each element of x. If w is missing then
          all elements of x are given the same weight. 

     ...: Arguments to be passed to methods (see
          'combineData-methods'): 

     '_t_r_i_m' the fraction (0 to 0.5, default is 0) of observations to be
          trimmed from each group of rows in 'x' according to 'y'. 

     '_n_a._r_m' logical; if 'TRUE', missing values are removed from 'x'
          and 'y' and 'z'. If 'FALSE' any missing values cause an
          error.

     '_e_l_e_m_e_n_t' which element of 'AssayData' to use for a given
          'ExpressionSet' input (default is '"exprs"') 

     '_f_e_a_t_u_r_e._g_r_o_u_p' which element of 'featureData' to use as binning
          variable (default is 'NULL'). Can be a character matching
          'varLabel' or simply an integer indicating which feature to
          choose. See 'getFeatures'. 

     '_e_l_e_m_e_n_t._w_e_i_g_h_t' which element of 'AssayData' to use for a given
          'ExpressionSet' input.  If 'NULL' (default), weighting is not
          performed. 

     '_f_e_a_t_u_r_e._w_e_i_g_h_t' which element of 'featureData' to use as
          weighting variable (default is 'NULL'). Can be a character
          matching 'varLabel' or simply an integer indicating which
          feature to choose. See 'getFeatures'. 

     '_s_a_m_p_l_e_s' which samples to use as data. Can be a vector of
          characters matching sample names, integers indicating which
          samples to choose, or a mixture of the two. If 'NULL'
          (default), all samples will be used.

     '...' other arguments not handled at this time.   

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

     Returns a matrix of combined numerical data, where each row
     represents the summary of a group of elements from the
     corresponding column in x.

_N_o_t_e:

     Each column in data matrix treated separately.

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

     Reid F. Thompson (rthompso@aecom.yu.edu)

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

     'combineData-methods', 'mean', 'weighted.mean'

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

     #demo(pipeline,package="HELP")

     x <- 1:100
     combineData(x,w=x/100)
     weighted.mean(x,w=x/100)

     y <- sample(c("a","b","c",1:3),size=100,replace=TRUE)
     combineData(cbind(x,x,2*x),y,trim=0.5)

     #rm(x,y)

