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 = "Target", 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 TargetID 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')

