twilight.permute.pair        package:twilight        R Documentation

_P_e_r_m_u_t_a_t_i_o_n _m_a_t_r_i_x _o_f _p_a_i_r_e_d _c_l_a_s_s _l_a_b_e_l_s

_D_e_s_c_r_i_p_t_i_o_n:

     The function returns a matrix where each row is a (un)balanced
     permutation of the input twosample class labels.

_U_s_a_g_e:

     twilight.permute.pair(v, m, bal = TRUE)

_A_r_g_u_m_e_n_t_s:

       v: A binary vector representing class labels in original order.
          Pairs must be in the same order. 

       m: A numerical value giving the number of permutations. 

     bal: Logical value. Results in balanced or unbalanced
          permutations. 

_V_a_l_u_e:

     Returns a matrix where each row contains one permuted vector of
     class labels. Note that even for balanced permutations, the first
     row always contains the original vector.

_A_u_t_h_o_r(_s):

     Stefanie Scheid <URL: http://www.molgen.mpg.de/~scheid>

_R_e_f_e_r_e_n_c_e_s:

     Scheid S and Spang R (2004): A stochastic downhill search
     algorithm for estimating the local false discovery rate, _IEEE
     TCBB_ *1(3)*, 98-108.

     Scheid S and Spang R (2005): twilight; a Bioconductor package for
     estimating the local false discovery rate, _Bioinformatics_
     *21(12)*, 2921-2922. 

     Scheid S and Spang R (2006): Permutation filtering: A novel
     concept for significance analysis of large-scale genomic data, in:
     Apostolico A, Guerra C, Istrail S, Pevzner P, and Waterman M
     (Eds.): _Research in Computational Molecular Biology: 10th Annual
     International Conference, Proceedings of RECOMB 2006, Venice,
     Italy, April 2-5, 2006_. Lecture Notes in Computer Science vol.
     3909, Springer, Heidelberg, pp. 338-347.

_S_e_e _A_l_s_o:

     'twilight.permute.unpair', 'twilight.combi'

