beadarrayMSV (version 1.0.2)

createAlleleSet: Create AlleleSetIllumina or MultiSet objects

Description

An "AlleleSetIllumina" (or "MultiSet") object is created, either by transforming a "BeadSetIllumina" object into an "AlleleSetIllumina" object, by reading from text-files containing pre-processed data, or by merging existing objects

Usage

createAlleleSet(BSData, beadInfo, normOpts, includeAB = FALSE)
createAlleleSetFromFiles(dataFiles, markers, arrays,
    phenoInfo = NULL, beadInfo = NULL, sep = "", quote = "")
createMultiSetFromFiles(dataFiles, markers, arrays,
    phenoInfo = NULL, beadInfo = NULL, sep = "", quote = "")
assignToAlleleSet(BSRed, BSAdd)
BSData{
    "BeadSetIllumina" object
  }
  beadInfo{
    Data-frame containing an entry for each marker, and the columns
    Name, SNP, ILMN.Strand,
    Address, Address2, and Norm.ID, as
    exported from Illumina's GenomeStudio Genotyping Module (or
    relatives). May also contain columns relating to genotype calls (see
    callGenotypes) 
  }
  normOpts{
    List containing at least the elements dist and
    pNorm (see setNormOptions)
  }
  includeAB{
    If TRUE, the Cartesian signal arrays A and B are
    returned as assayData entries in the new
    "AlleleSetIllumina" object 
  }
  dataFiles{
    Character vector containing filenames where the different
    data-tables are saved (see makeFilenames)
  }
  markers{
    Index to markers in the dataFiles files
  }
  arrays{
    Index to arrays/samples in the dataFiles files
  }
  phenoInfo{
    Data-table with phenotype data. Argument is ignored if phFile is provided in
    dataFiles
  }
  sep{
    Field delimiter in text-files (see read.table)
  }
  quote{
    Quote-marks used for character strings (see read.table)
  }
  BSRed{
    "AlleleSetIllumina" object
  }
  BSAdd{
    "AlleleSetIllumina" object with data to
    include in BSRed
  }
A "BeadSetIllumina" object contains bead-type information,
  whereas an "AlleleSetIllumina" object contains marker
  information (for each Infinum I marker, there are two
  bead-types). The function createAlleleSet takes a
  "BeadSetIllumina" object as input and merges the
  R and G intensities into A and B
  intensities. The former relates to bead-types and the latter relates
  to markers as defined in beadInfo. The required polar
  coordinate intensities intensity and theta are
  estimated based on A and B, and depend on the
  distance measures defined in normOpts. The angles theta
  are scaled such that {0, 90} degrees are represented by {0, 1},
  and intensity vs. theta for single markers are
  usually plotted on Cartesian axes for genotype calling.
  If data-files are available for all required assayData,
  phenoData, and featureData elements, an
  "AlleleSetIllumina" or a
  "MultiSet" object may be constructed
  with create-AlleleSetFromFiles or
  createMultiSetFromFiles, respectively. The former has three
  required assayData elements whereas the latter has none.
  
  Sometimes, and in particular after manual genotype calling, there is a
  need to update an "AlleleSetIllumina" object with new
  information. The function assignToAlleleSet adds any
  data in BSAdd to BSRed, overwriting previous data if
  there is a conflict
Object of class "AlleleSetIllumina" or "MultiSet"
L. Gidskehaug, M. Kent, B. Hayes, and S. Lien. Genotype calling and
  mapping of multisite variants using an Atlantic salmon iSelect
  SNP-array. Submitted
[object Object]
AlleleSetIllumina,
MultiSet, writeAlleleSet,
makeFilenames
#Read raw data files into BeadSetIllumina object
rPath <- system.file("extdata", package="beadarrayMSV")
BSDataRaw <- readBeadSummaryOutput(path=rPath,recursive=TRUE)
#Find indexes to sub-bead pools
beadInfo <- read.table(paste(rPath,'beadData.txt',sep='/'),sep='\t',
    header=TRUE,as.is=TRUE)
rownames(beadInfo) <- make.names(beadInfo$Name)
normInd <- getNormInd(beadInfo,featureNames(BSDataRaw))
#Pre-process BSData
normOpts <- setNormOptions(minSize=10)
plotPreprocessing(BSDataRaw,normInd,normOpts,plotArray=1)
BSData <- preprocessBeadSet(BSDataRaw,normInd,normOpts)
print(BSData)
print(fData(BSData)[1:10,])
print(fvarMetadata(BSData))
#Convert to AlleleSetIllumina-object
BSRed <- createAlleleSet(BSData,beadInfo,normOpts)
print(BSRed)
print(fData(BSRed)[1:10,])
print(fvarMetadata(BSRed))
#Read pre-processed data directly into AlleleSetIllumina object
dataFiles <- makeFilenames('testdata',normOpts,rPath)
beadFile <- paste(rPath,'beadData_testdata.txt',sep='/')
beadInfo2 <- read.table(beadFile,sep='\t',header=TRUE,as.is=TRUE)
BSRed <- createAlleleSetFromFiles(dataFiles[1:4],beadInfo=beadInfo2)
print(varLabels(BSRed))