produceGEOPlatformFile         package:lumi         R Documentation

_P_r_o_d_u_c_e _G_E_O _P_l_a_t_f_o_r_m _S_u_b_m_i_s_s_i_o_n _F_i_l_e _i_n _S_O_F_T _f_o_r_m_a_t

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

     Produce GEO Sample Submission File in SOFT format based on the
     provided LumiBatch object and Illumina ID Mapping library

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

     produceGEOPlatformFile(x.lumi, lib.mapping = NULL, nuIDMode = FALSE, fileName = "GEOPlatformFile.txt")

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

  x.lumi: The LumiBatch object keeping all probes 

lib.mapping: The Illumina ID Mapping library, e.g.,
          "lumiHumanIDMapping" 

nuIDMode: Determine whether producing the platform indexed by nuID 

fileName: Filename of the GEO Platform File name 

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

     The function produces the GEO platform submission file based on
     the chip information kept in the Illumina ID Mapping library
     (specified by lib.mapping parameter). The determination of chip
     type will be automatically done by selecting the best matching of
     the probe IDs with individual chips.

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

     Save the result as a text file in SOFT platform submission format.

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

     Pan Du

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

     http://www.ncbi.nlm.nih.gov/projects/geo/info/soft2.html

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

     'produceGEOSubmissionFile'

