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 = TRUE, includeAllChipProbe=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 

includeAllChipProbe: Determine whether including all probes in the
          Manifest file or just the probes used in the x.lumi object 

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'

_E_x_a_m_p_l_e_s:

     # data(example.lumi)
     # produceGEOPlatformFile(example.lumi, lib.mapping='lumiHumanIDMapping')

