calcPrototype              package:HELP              R Documentation

_C_a_l_c_u_l_a_t_e _p_r_o_t_o_t_y_p_e

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

     Calculates prototype (trimmed mean) across all samples

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

     calcPrototype(x, ...)

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

       x: a numeric matrix, where each column represents a different
          sample 

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

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

     '_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.

     '_c_e_n_t_e_r' logical; if 'TRUE' (default) samples will be
          mean-centered before protototype calculation. If 'FALSE',
          this mean-centering step will be skipped 

     '_t_r_i_m' the fraction (0 to 0.5, default is 0.1) of observations to
          be trimmed from each end of each row and column in 'x' before
          the mean is computed. 

     '_v_e_r_b_o_s_e' logical; if 'TRUE' (default) progress will be output to
          screen. If 'FALSE', no output will be displayed.

     '...' other arguments to be passed to 'mean'. See 'mean'. 

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

     Returns a vector of numerical data, representing the prototype
     ([trimmed] mean) of all samples in x.

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

     Mark Reimers (mreimers@vcu.edu), Reid F. Thompson
     (rthompso@aecom.yu.edu)

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

     'calcPrototype-methods', 'mean'

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

     #demo(pipeline,package="HELP")

     x <- matrix(data=rep(1:1000,10),nrow=1000,ncol=10)
     x <- x*(sample(1:100/100,size=10000,replace=TRUE))
     x <- t(t(x)-1000*(1:10))
     x[c(1:10,991:1000),]
     x.avg <- calcPrototype(x)
     x.avg[c(1:10,991:1000)]

     #rm(x,x.avg)

