calcTNullFast           package:sigPathway           R Documentation

_C_o_m_p_u_t_e _N_u_l_l _T _D_i_s_t_r_i_b_u_t_i_o_n _f_o_r _E_a_c_h _G_e_n_e

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

     Computes a null t distribution for each gene by permuting the
     phenotypes.

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

     calcTNullFast(tab, phenotype, nsim, ngroups = 2, allphenotypes = FALSE)

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

     tab: a numeric matrix of expression values, with the rows and
          columns representing probe sets and sample arrays,
          respectively

phenotype: a numeric (or character if 'ngroups' >= 2) vector indicating
          the phenotype

    nsim: an integer indicating the number of permutations to use

 ngroups: an integer indicating the number of groups in the expression
          matrix

allphenotypes: a boolean indicating whether the function should
          consider all possible permutations of the phenotype,
          including the original, non-permuted phenotype

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

     Similar to 'calcTStatFast' but calculates t-statistics over
     permuted phenotypes.  If 'allphenotypes == FALSE', then any
     permutation that has a permuted phenotype equal to the original
     phenotype will be repermuted.  For example, all the possible
     permutations for 'phenotype == c(0,0,1,1)' are 'c(0,0,1,1)',
     'c(0,1,0,1)', 'c(1,0,1,0)', 'c(1,0,0,1)', 'c(0,1,1,0)', and
     'c(1,1,0,0)'.  If 'allphenotypes == FALSE', then the results will
     not include values from the 'c(0,0,1,1)' case.

     The help file of 'calcTStatFast' has more details on the different
     statistics one can calculate based on the value specified for
     'ngroups'.

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

     A matrix with 'nsim' rows and 'nrow(tab)' columns.

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

     Weil Lai

