prep               package:pcaMethods               R Documentation

_P_r_e_p_r_o_c_e_s_s _a _m_a_t_r_i_x _f_o_r _P_C_A

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

     Implements simple preprocessing alternatives for scaling a matrix.

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

     prep(object, scale=c("none", "pareto", "vector", "UV"), center=TRUE, ...)

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

  object: Numerical matrix  with (or an object coercible to such) with
          samples in rows and variables as columns. Also takes
          'exprSet' in which case the transposed 'exprs' slot is used.

  center: Indicates if the matrix should be mean centred or not.

   scale: One of "UV" (unit variance a=a/sigma_{a}) "vector" (vector
          normalisation b=b/||b||), "pareto" or "none" to indicate
          which scaling should be used to scale the matrix with a
          variables and b samples.

     ...: Only used for passing through arguments.

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

     Does basically the same as 'scale' but adds some alternative
     scaling options.

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

     A matrix with attribute "scaled:center" if centring was done.

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

     Wolfram Stacklies, Henning Redestig

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

     'scale'

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

     object <- matrix(rnorm(50), nrow=10)
     object <- prep(object, scale="vector", center=TRUE)

