sage.library.comparison      package:sagenhaft      R Documentation

_C_l_a_s_s _s_a_g_e._l_i_b_r_a_r_y._c_o_m_p_a_r_i_s_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Class for storing the data of a pairwise comparison between two
     SAGE libraries.

_U_s_a_g_e:

     read.sage.library.comparison(file)
     write.sage.library.comparison(x, file=paste(x$name, "sagecomp", sep="."))
     compare.lib.pair(lib1, lib2) 

_A_r_g_u_m_e_n_t_s:

x,lib1,lib2: A sage library object

    file: File name to read or write to

_D_e_t_a_i_l_s:

     SAGE library comparison objects consists of one data.frames. It
     stores a A and an M value which are the log2 average expression
     and log2 ratio, respectively. It also has a column for the
     resulting p.values from 'sage.test'.
     'read.sage.library.comparison' and 'write.sage.library.comparison'
     are utility functions to read and write SAGE library comparisons.
     'compare.lib.pair' can be used to generate SAGE library
     comparisons.

_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:

     'sage.test'

_E_x_a_m_p_l_e_s:

     library(sagenhaft)
     B6Hypo <- read.sage.library(system.file("data/B6HypothalHFI.sage",
                                 package="sagenhaft")) 
     E15post <- read.sage.library(system.file("data/E15postHFI.sage",
                                  package="sagenhaft")) 
     libcomp <- compare.lib.pair(B6Hypo, E15post)
     plot(libcomp)
     libcomp

