sage.library            package:sagenhaft            R Documentation

_C_l_a_s_s _s_a_g_e._l_i_b_r_a_r_y

_D_e_s_c_r_i_p_t_i_o_n:

     The SAGE library class contains all the data and annotation for a
     SAGE library. It can contain two data.frames.

_U_s_a_g_e:

     read.sage.library(file)
     write.sage.library(x, file=paste(x$libname, "sage", sep="."),
                        what="complete") 

_A_r_g_u_m_e_n_t_s:

       x: A sage library object

    file: File name to read or write to

    what: "complete", read complete librarary tags and sequences;
          "tags", read only tags and counts

_D_e_t_a_i_l_s:

     SAGE library objects consists of one or two data.frames. The
     data.frame "tags" contains all the unique tags in the library and
     its counts. The data.frame "seqs" contains all the individual tag
     sequences and associated quality values. 'read.sage.library' and
     'write.sage.library' are utility functions to read and write SAGE
     libraries.

_A_u_t_h_o_r(_s):

     Tim Beissbarth

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://tagcalling.mbgproject.org>

_S_e_e _A_l_s_o:

     'extract.lib'

_E_x_a_m_p_l_e_s:

     library(sagenhaft)
     E15postHFI <- read.sage.library(system.file("data/E15postHFI.sage",
                                     package="sagenhaft")) 
     E15postHFI

