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

