DNASuffixArray          package:Biostrings          R Documentation

_f_u_n_c_t_i_o_n _t_o _c_r_e_a_t_e _a _s_u_f_f_i_x _a_r_r_a_y _f_o_r _a _D_N_A _s_t_r_i_n_g

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

     This function creates a suffix array for the given DNA strings.
     The sorting of the suffix array can be done based on a given
     number of letters at the beginning of each suffix.

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

     DNASuffixArray(x, prefixLength = max(nchar(x)))

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

       x: an object of class "BioString" representing one or more DNA
          strings. If its length is more than one, suffix arrays for
          each of the string are created and merged. 

prefixLength: the number of letters at the beginning of each suffix
          that are used in sorting the suffix array. 

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

     An object of class "BioString", with the suffixes from the
     argument sorted in increasing order. For the purpose of sorting,
     each string is assumed to be padded at the end with a letter lower
     in order than any letter in the alphabet of the string.

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

     Saikat DebRoy

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

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

     'sortDNAString' for sorting the strings in an object of class
     "BioString".

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

     data('yeastSEQCHR1')
     yeast1 <- DNAString(yeastSEQCHR1)
     DNASuffixArray(substr(yeast1, 1, 30))
     x <- substring(yeast1, c(1, 16), c(15, 30))
     x
     DNASuffixArray(x)

