getNormFactor           package:SAGElyzer           R Documentation

_F_u_n_c_t_i_o_n_s _t_h_a_t _g_e_t _n_o_r_m_a_l_i_z_a_t_i_o_n _f_a_c_t_o_r_s _f_o_r _S_A_G_E _l_i_b_r_a_r_i_e_s

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

     SAGE libraries vary in the total number of tags so that counts
     need to be normalized across libraries. These functions get the
     normalization factors that are stored in a database table.

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

     getNormFactor(normalize = c("min", "max", "none"), libs)
     queryInfoDB(libCol = "libname",
                             infoCol = c("filename", "minfactor", "maxfactor"))

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

normalize: 'normalize' a character string for the means of
          normalization. Have to be either "min", "max", or "none"

    libs: 'libs' a vector of character strings for the names of SAGE
          libraries to be normalized

  libCol: 'libCol' a character string for the name of the column in a
          database table where names of SAGE libraries are stored

 infoCol: 'infoCol' a vector of character strings for the names of
          database columns where SAGE library information is kept

_D_e_t_a_i_l_s:

     The normalization factor is calculated by dividing the total
     number of tags for a given library by the maximum or minimum value
     across the library.

     'getNormFactor' returns the normalization factors for a given set
     of SAGE libraries.

     'queryInfoDB' queries a database table containing information
     about SAGE libries to get the normalization factor for SAGE
     libraries.

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

     Both 'getNormFactor' and  'queryInfoDB' return a data frame
     containing normalization factors for a set of SAGE libraries.

_N_o_t_e:

     The functions are part of the Bioconductor project at Dana-Farber
     Cancer Institute to provide Bioinformatics functionalities through
     R

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

     Jianhua Zhang

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

     <URL: http://www.ncbi.nlm.nih.gov/SAGE/>

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

     'SAGELyzer'

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

     # No example is given as database support is required

