addNuID2lumi              package:lumi              R Documentation

_A_d_d _t_h_e _n_u_I_D _i_n_f_o_r_m_a_t_i_o_n _t_o _t_h_e _L_u_m_i_B_a_t_c_h _o_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     Replace the Illumina Id (Target ID or Probe Id) as nuID
     (nucleotide universal identifier) for indexing genes in the
     LumiBatch object

_U_s_a_g_e:

     addNuID2lumi(x.lumi, annotationFile=NULL, sep = NULL, lib.mapping = NULL,  annotationColName = c(sequence = "Probe_Sequence", target = "ILMN_Gene", probe='Probe_Id'), verbose = TRUE)

_A_r_g_u_m_e_n_t_s:

  x.lumi: a LumiBatch object 

annotationFile: a annotation file, which includes the Illumina ID
          (target or probe ids) and probe sequence information

     sep: the separation used in the annotation file. Automatically
          detect the separator if it is "," or "\t". 

lib.mapping: a Illumina ID mapping package, e.g, lumiHumanIDMapping 

annotationColName: the annotation column name in the annotation file
          used for the probe sequence and TargetID and ProbeID 

 verbose: a boolean to decide whether to print out some messages 

_D_e_t_a_i_l_s:

     Since the default Illumina IDs (TargetID (ILMN_Gene ID) and
     ProbeId (Probe_Id)) are not consistent between different arrays
     and batches, we invented a nuID, which is one-to-one matching with
     the probe sequence. This function is to replace the Illumina ID
     with the nuID. If the annotation library (the unzipped manifest
     file (.bgx)) is provided, the function will automatically check
     whether the Illumina ID is provided for the microarray data. We
     recommend output the data using ProbeID when using Illumina
     BeadStudio software, because the TargetID (ILMN_Gene ID) are not
     unique.

_V_a_l_u_e:

     a LumiBatch object with Illumina ID replaced by nuID.

_A_u_t_h_o_r(_s):

     Pan Du

_R_e_f_e_r_e_n_c_e_s:

     Du, P., Kibbe, W.A., Lin, S.M., "nuID: A universal naming schema
     of oligonucleotides for Illumina, Affymetrix, and other
     microarrays", submitted.

_S_e_e _A_l_s_o:

     'IlluminaID2nuID', 'lumiR'

_E_x_a_m_p_l_e_s:

     ## load example data
     # data(example.lumi)

     ## specify the annotation file for the Illumina chip
     # annotationFile <- 'Human_RefSeq-8.csv'
     ## Replace the Target ID with nuID
     # lumi.nuID <- addNuID2lumi(example.lumi, annotationFile)

     ## An alternative way is to load the Annotation library and match the targetID (or Probe Id) with nuID
     # lumi.nuId <- addNuID2lumi(example.lumi, lib.mapping='lumiHumanIDMapping')

