lumiR                  package:lumi                  R Documentation

_R_e_a_d _i_n _I_l_l_u_m_i_n_a _e_x_p_r_e_s_s_i_o_n _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     Read in Illumina expression data. We assume the data was saved in
     a comma or tab separated text file.

_U_s_a_g_e:

     lumiR(fileName, sep = NULL, detectionTh = 0.01, na.rm = TRUE, convertNuID = TRUE, lib.mapping = NULL, dec = '.', parseColumnName = FALSE, checkDupId = TRUE,
     QC = TRUE, columnNameGrepPattern = list(exprs='AVG_SIGNAL', se.exprs='BEAD_STD', detection='DETECTION', beadNum='Avg_NBEADS'),
     inputAnnotation=TRUE, annotationColumn=c('ACCESSION', 'SYMBOL', 'PROBE_SEQUENCE', 'PROBE_START', 'CHROMOSOME', 'PROBE_CHR_ORIENTATION', 'PROBE_COORDINATES', 'DEFINITION'), verbose = TRUE, ...)

_A_r_g_u_m_e_n_t_s:

fileName: fileName of the data file 

     sep: the separation character used in the text file.  

detectionTh: the p-value threshold of determining detectability of the
          expression. See more details in 'lumiQ' 

   na.rm: determine whether to remove NA 

convertNuID: determine whether convert the probe identifier as nuID 

lib.mapping: a Illumina ID mapping package, e.g, lumiHumanIDMapping,
          used by 'addNuID2lumi' 

     dec: the character used in the file for decimal points.

parseColumnName: determine whether to parse the column names and
          retrieve the sample information (Assume the sample
          information is separated by "_".) 

checkDupId: determine whether to check duplicated TargetIDs or
          ProbeIds. The duplicated ones will be averaged.

      QC: determine whether to do quality control assessment after read
          in the data.

columnNameGrepPattern: the string grep patterns used to determine the
          slot corresponding columns.

inputAnnotation: determine whether input the annotation information
          outputted by BeadStudio if exists.

annotationColumn: the column names of the annotation information
          outputted by BeadStudio

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

     ...: other parameters used by 'read.table' function 

_D_e_t_a_i_l_s:

     The function can automatically determine the separation character
     if it is Tab or comma. Otherwise, the user should specify the
     separator manually. If the annotation library is provided, the
     Illumina Id will be replaced with nuID, which is used as the index
     Id for the lumi annotation packages. If the annotation library is
     not provided, it will try to directly convert the probe sequence
     (if provided in the BeadStudio output file) as nuIDs.

     The parameter "columnNameGrepPattern" is designed for some
     advanced users. It defines the string grep patterns used to
     determine the slot corresponding columns. For example, for the
     "exprs" slot in LumiBatch object, it is composed of the columns
     whose name includes "AVG_SIGNAL". In some cases, the user may not
     want to read the "detection" and "beadNum" related columns to save
     memory. The user can set the "detection" and "beadNum" as NA in
     "columnNameGrepPattern". If the 'se.exprs' is set as NA or the
     corresponding columns are not available, then lumiR will create a
     ExpressionSet object instead of LumiBatch object.

     The parameter "parseColumnName" is designed to parse the column
     names and retrieve the sample information. We assume the sample
     information is separated by "_" and the last element after "_" is
     the sample label (sample names of the LumiBatch object).  If the
     parsed sample labels are not unique, then the entire string will
     be used as the sample label. For example: "1881436055_A_STA 27aR"
     is included in one of the column names of BeadStudio output file.
     Here, the program will first treat "STA 27aR" as the sample label.
     If it is not unique across the samples, "1881436055_A_STA 27aR"
     will be the sample label. If it is still not unique, the program
     will report warning messages. All the parsed information is kept
     in the phenoData slot. By default, "parseColumnName" is FALSE. We
     suggest the users use it only when they know what they are doing.

     Current version of lumiR can adaptively read the output of
     BeadStudio Verson 1 and 3. The format Version 3 made quite a few
     changes comparing with previous versions. One change is the
     detection value. It was called detectable when the detection value
     is close to one for Version 1 format. However, the detection value
     became a p-value in the Version 3. As a result, the detectionTh is
     automatically changed based on the version. The detectionTh 0.01
     for the Version 3 will be changed as the detectionTh 0.99 for
     Version 1. Another big change is that Version 3 separately output
     the control probe (gene) information and a "Samples Table". As a
     result, the controlData slot in LumiBatch class was added to keep
     the control probe (gene) information, and a QC slot to keep the
     quality control information, including the "Sample Table" output
     by BeadStudio version 3.

     The recent version of BeadStudio can also output the annotation
     information together with the expression data. In the users also
     want to input the annotation information, they can set the
     parameter "inputAnnotation" as TRUE. At the same time, they can
     also specify which columns to be inputted by setting parameter
     "annotationColumn". The BeadStudio annotation columns include:
     SPECIES, TRANSCRIPT, ILMN_GENE, UNIGENE_ID, GI, ACCESSION, SYMBOL,
     PROBE_ID, ARRAY_ADDRESS_ID, PROBE_TYPE, PROBE_START,
     PROBE_SEQUENCE, CHROMOSOME, PROBE_CHR_ORIENTATION,
     PROBE_COORDINATES, DEFINITION, ONTOLOGY_COMPONENT,
     ONTOLOGY_PROCESS, ONTOLOGY_FUNCTION, SYNONYMS, OBSOLETE_PROBE_ID.
     As the annotation data is huge, by default, we only input:
     ACCESSION, SYMBOL, PROBE_START, CHROMOSOME, PROBE_CHR_ORIENTATION,
     PROBE_COORDINATES, DEFINITION. As some annotation information may
     be outdated. We recommend using Bioconductor annotation packages
     to retrieve the annotation information.

_V_a_l_u_e:

     return a LumiBatch object

_A_u_t_h_o_r(_s):

     Simon Lin, Pan Du

_S_e_e _A_l_s_o:

     'LumiBatch', 'addNuID2lumi'

_E_x_a_m_p_l_e_s:

     ## specify the file name
     # fileName <- 'Barnes_gene_profile.txt' # Not Run
     ## load the data
     # x.lumi <- lumiR(fileName)

     ## load the data with empty detection and beadNum slots
     # x.lumi <- lumiR(fileName, columnNameGrepPattern=list(detection=NA, beadNum=NA))

