comp.unadjp               package:DEDS               R Documentation

_C_o_m_p_u_t_i_n_g _p_e_r_m_u_t_a_t_i_o_n _b_a_s_e_d _u_n_a_d_j_u_s_t_e_d _p _v_a_l_u_e_s _f_o_r _e_a_c_h _r_o_w _o_f _a _m_a_t_r_i_x

_D_e_s_c_r_i_p_t_i_o_n:

     This function computes permuation based unadjusted p values for a
     selected test statistic, e.g., one- or two-sample t-statitics,
     F-statistics, SAM, Fold change, for each row of a matrix.

_U_s_a_g_e:

     comp.unadjp(X, L, B = 1000, test = c("t", "fc", "sam", "f"), tail = c("abs", "lower", "higher"), extra = NULL)

_A_r_g_u_m_e_n_t_s:

       X: A  matrix, with m rows corresponding to variables
          (hypotheses) andn columns corresponding to observations. In
          the case of gene expression data, rows correspond to genes
          and columns to mRNA samples. The data can be read using
          'read.table'. 

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

       B: The number of permutations. For a complete enumeration, 'B'
          should be 0 (zero) or any number not less than the total
          number of permutations. 

    test: A character string specifying the statistic to be used to
          test the null hypothesis of no association between the
          variables and the class labels.
           If 'test="t"', for one-class, the tests are based on
          one-sample t-statistics; for two-class, the tests are based
          on two-sample t-statistics (unequal variances).  
           If 'test="f"', the tests are based on F-statistics.
           If 'test="fc"', the tests are based on fold changes among
          classes.
           If 'test="sam"', the tests are based on SAM-statistics. 

    tail: A character string specifying the type of rejection region.
           If 'side="abs"', two-tailed tests, the null hypothesis is
          rejected for large absolute values of the test statistic.
           If 'side="higher"', one-tailed tests, the null hypothesis is
          rejected for large values of the test statistic.
           If 'side="lower"', one-tailed tests,  the null hypothesis is
          rejected for small values of the test statistic. 

   extra: Extra parameter need for the test specified; see
          'deds.genExtra'.

_D_e_t_a_i_l_s:

     The function 'comp.unadjp' computes unadjusted p values using a
     permutation scheme.

_V_a_l_u_e:

     A vector of unadjusted p values for each row of the 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:

     'deds.genExtra', 'comp.stat'

_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

     # t statistics
     unadjp.t <- comp.unadjp(X, L, test="t")

