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 = NULL,  annotationColName = c(sequence = "Probe_Sequence", target = "Target", probe='ProbeId'))

_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: a lumi annotation package 

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

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

     Since the default TargetID and ProbeId 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 TargetID (or ProbeID) with the nuID. If the annotation
     library is provided, the function will automatically check whether
     the TargetID or ProbeID is provided for the microarray data. We
     recommend output the data using ProbeID when using Illumina
     BeadStudio software, because the TargetID are not unique.

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

     a LumiBatch object with TargetID (or ProbeID) 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:

     '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='lumiHumanV1')

