produceGEOSubmissionFile        package:lumi        R Documentation

_P_r_o_d_u_c_e _G_E_O _S_a_m_p_l_e _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 the SOFT format based on the
     provided LumiBatch object and sample information

_U_s_a_g_e:

     produceGEOSubmissionFile(lumiNormalized, lumiRaw, lib.mapping = NULL, idType = 'Probe', sampleInfo = NULL, fileName = "GEOSubmissionFile.txt", supplementaryRdata = TRUE, ...)

_A_r_g_u_m_e_n_t_s:

lumiNormalized: The normalized data (LumiBatch object) 

 lumiRaw: The raw data (LumiBatch object), e.g., returned by 'lumiR' 

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

  idType: the idType parameter of function 'nuID2IlluminaID' 

sampleInfo: The sample information filename or data.frame, which is
          returned by 'produceGEOSampleInfoTemplate' 

fileName: The file name of GEO Submission file  

supplementaryRdata: determine whether produce the Rdata supplement
          data, which include both lumiNormalized and lumiRaw R
          objects. 

     ...: other parameters used by function 'nuID2IlluminaID' 

_D_e_t_a_i_l_s:

     The function produces the GEO sample submission file including
     both normalized and raw data information  in the SOFT format. The
     sample information should be provided by the user as a data.frame
     or Tab separated text file following the format of the template,
     which can be produced by function 'produceGEOSampleInfoTemplate'.
     Users need to fill in the detailed sample descriptions in the
     template, especially the Sample_title, Sample_description and some
     protocols. Users are also suggested to fill in the
     "Sample_platform_id" by checking information of the GEO Illumina
     platform.

     When the parameter "supplementaryRdata" is TRUE, the R objects,
     lumiNormalized, lumiRaw and sampleInfo, will be saved in a file
     named 'supplementaryData.Rdata'.

_V_a_l_u_e:

     Save the result as a text file in SOFT sample submission format.
     The supplementary Rdata will be saved in a file
     'supplementaryData.Rdata'.

_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:

     'produceGEOSampleInfoTemplate', 'produceGEOPlatformFile'

_E_x_a_m_p_l_e_s:

     ## Not run
     ## Produce the sample information template
     # produceGEOSampleInfoTemplate(lumiNormalized, lib.mapping = NULL, fileName = "GEOsampleInfo.txt")
     ## After editing the 'GEOsampleInfo.txt' by filling in sample information
     # produceGEOSubmissionFile(lumiNormalized, lumiRaw, lib='lumiHumanIDMapping', sampleInfo='GEOsampleInfo.txt')

