pwm-class              package:seqLogo              R Documentation

_C_l_a_s_s "_p_w_m"

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

     An object of class '"pwm"' represents the 4xW position weight
     matrix of a DNA sequence motif. The entry in row i, column j gives
     the probability of observing nucleotide 'c("A","C","G","T")[i]' in
     position j of the motif.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("pwm", ...)'.

_S_l_o_t_s:

     '_p_w_m': Object of class '"matrix"' The position weight matrix.

     '_w_i_d_t_h': '"numeric"' The width of the motif.

     '_a_l_p_h_a_b_e_t': '"character"' The sequence alphabet. Currently, only
          "DNA" is supported.

_M_e_t_h_o_d_s:

_s_u_m_m_a_r_y 'signature(object = "pwm",...)' Prints the position weight
     matrix. 

_p_r_i_n_t 'signature(x = "pwm",...)' Prints the position weight matrix.

_s_h_o_w 'signature(object = "pwm")' Prints the position weight matrix. 

_p_l_o_t 'signature(x = "pwm")' Plots the sequence logo of the position
     weight matrix. 

_N_o_t_e:

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

     Oliver Bembom, bembom@berkeley.edu

_R_e_f_e_r_e_n_c_e_s:

_S_e_e _A_l_s_o:

_E_x_a_m_p_l_e_s:

