comp.FC                 package:DEDS                 R Documentation

_C_o_m_p_u_t_i_n_g _F_o_l_d _C_h_a_n_g_e _f_o_r _D_i_f_f_e_r_e_n_t_i_a_l _E_x_p_r_e_s_s_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     'comp.FC' returns a function of one argument with bindings for
     'L', 'is.log' and 'FUN'. This function accepts a microarray data
     matrix as its single argment, when evaluated, computes fold change
     for each row of the matrix.

_U_s_a_g_e:

     comp.FC(L = NULL, is.log = TRUE, FUN = mean)

_A_r_g_u_m_e_n_t_s:

       L: A vector of integers corresponding to observation (column)
          class labels. For k classes, the labels must be integers
          between 0 and k-1.

  is.log: A logical variable indicating whether the data has been
          logged.

     FUN: The summary statistics function used to calcuate fold change,
          the default is set as 'mean', the user can also use 'median'

     .

_D_e_t_a_i_l_s:

     The function returned by 'comp.FC' calculates fold change for each
     row of the matrix, given specific class labels. If 'is.log=TRUE',
     fold change is calculated by substraction; if 'is.log=FALSE', fold
     change is calculated by division.

_V_a_l_u_e:

     'comp.FC' returns a function with bindings for 'L', 'is.log' and
     'FUN', which calculates and returns a vector of fold changes for
     each row in the data matrix.

_A_u_t_h_o_r(_s):

     Yuanyuan Xiao, yxiao@itsa.ucsf.edu, 
      Jean Yee Hwa Yang, jean@biostat.ucsf.edu.

_S_e_e _A_l_s_o:

     'comp.t','comp.F'

_E_x_a_m_p_l_e_s:

     X <- matrix(rnorm(1000,0,0.5), nc=10)
     L <- rep(0:1,c(5,5))

     # genes 1-10 are differentially expressed
     X[1:10,6:10]<-X[1:10,6:10]+1

     f <- comp.FC(L=L)
     f.X <- f(X)

