sage.utilities           package:sagenhaft           R Documentation

_U_t_i_l_i_t_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Different utilities to use with SAGE data.

_U_s_a_g_e:

     tagnum2tagmatrix(tags, length)
     tagmatrix2tagnum(tags, length=ncol(tags))
     tagnum2tagsequence(tags, length)
     tagsequence2tagnum(tags, length)
     revcomp(seq)

_A_r_g_u_m_e_n_t_s:

    tags: integer or character vector giving SAGE tags.

  length: Length of SAGE tags.

     seq: Character vector or list of sequences.

     ...: SAGE library objects.

_D_e_t_a_i_l_s:

     These functions are utility functions used in SAGE tag extraction,
     e.g. to convert SAGE tag sequences to numeric values, i.e. base 4
     for efficient storage and handling, and to reverse complement
     sequences.

_A_u_t_h_o_r(_s):

     Tim Beissbarth

_E_x_a_m_p_l_e_s:

     library(sagenhaft)
     tags <- c("aaa", "ttt", "ccc")
     tagsnumeric <- tagsequence2tagnum(tags, 3)
     tagsmatrix <- tagnum2tagmatrix(tagsnumeric, 3)
     tags <- tagnum2tagsequence(tagmatrix2tagnum(tagsmatrix, 3), 3)
     revcomp(tags)

