beadarrayMSV (version 1.0.3)

translateTheta: Convert genotype calls to allele information

Description

Genotype calls represented as numeric values (allele ratios) within [0, 1] are converted to character strings containing allele information A, T, C, and G

Usage

translateTheta(calls, resInfo, type = "regular")
translateThetaCombined(BSRed, mergedCalls = NULL)
translateThetaFromFiles(dataFiles, mergedCalls = NULL,
    markerStep = 1000, sep = "", quote = "")
calls{
    Numeric matrix with calls {0, 1/2, 1} representing allele ratios for each
    sample. Each row is a unique marker or paralogue (specified with type)
  }
  resInfo{
    Data table containing featureData, including the columns
    Classification, SNP, and
    ILMN.Strand. These hold the genotype categories from
    callGenotypes and the SNP and
    TOP/BOT-category of the BeadArray markers (see
    createAlleleSet)
  }
  type{
    One of regular, single, or merged (see
    details below)
  }
  BSRed{
    "AlleleSetIllumina" object containing an
    assayData entry call and a featureData column
    Classification (see callGenotypes)
  }
  mergedCalls{
    Matrix with calls from resolved MSV-5 paralogs (see
    assignParalogues)
  }
  dataFiles{
    Character vector containing file names (see makeFilenames)
  }
  markerStep{
    The maximum number of markers loaded into the workspace at the time
  }
  sep{
    Field delimiter in text-files (see read.table)
  }
  quote{
    Quote-marks used for character strings (see read.table)
  }
The main difference between translateTheta and
  translateThetaCombined is that the former can only handle
  call-values {0, 1/2, 2} whereas the latter handles values
  {0, 1/4, 1/2, 3/4, 1}. In effect this means that markers from
  duplicated genome regions have to be handled in a special way if
  analysed with translateTheta. If type == "regular", the
  markers are treated as if they were all from 
  a diploid region. This implies that all non-segregating paralogs of
  MSV-a and MSV-b markers are ignored, effectively
  turning these markers into SNPs. Markers classified as
  MSV-5 or PSV are set to missing (see
  makeDiploidCalls). If type == "single",
  calls is expected to contain resolved MSV-5 paralogs named
  with -Para1 or -Para2 (see
  unmixParalogues). If type == "merged",
  resolved MSV-5 paralogs named according to their respective
  chromosomes, -ChromX, are expected (see
  assignParalogues). The main use of this function is to
  prepare genotype calls for mapping software which requires diploid
  markers. 
  With translateThetaCombined, there is always one element per
  marker, as required by the "AlleleSetIllumina". If
  mergedCalls is given, the MSV-5 paralogs will be
  resolved, otherwise only the ratio of the alleles across paralogs will
  be returned. The function translateThetaFromFiles performs the
  same operations on data sequentially loaded into the workspace, and
  the genotypes are written to file dataFiles$genoFile as they
  are found.
Output from translateTheta is a matrix whose dimensions depend
  on the input data. If calls has one row per marker (i.e. type
  == "regular"), the number of rows in the output matrix also
  equals the number of markers. If calls has one row per
  paralogue (i.e. type != "regular"), the number of rows
  in the output matrix also equals the number of paralogs. Each element
  is a character string x y denoting the two alleles
  (A, T, C, G, or - for
  missing).
  In contrast, the output from translateThetaCombined is an
  AlleleSetIllumina object with an added assayData
  entry genotype. The elements of this matrix representing
  diploid markers are given as xy, un-resolved tetraploid markers
  are given as xyzw, and resolved tetraploid markers are given
  as xy,zw (paralogs separated by comma). The letters
  correspond to any of the 4 bases or - for missing.
  The function translateThetaFromFiles are used for its side
  effects.
[object Object]
makeDiploidCalls, unmixParalogues,
  assignParalogues, makeFilenames,
  callGenotypes
#Read 25 markers into an AlleleSetIllumina object
rPath <- system.file("extdata", package="beadarrayMSV")
normOpts <- setNormOptions()
dataFiles <- makeFilenames('testdata',normOpts,rPath)
beadFile <- paste(rPath,'beadData_testdata.txt',sep='/')
beadInfo <- read.table(beadFile,sep='\t',header=TRUE,as.is=TRUE)
BSRed <- createAlleleSetFromFiles(dataFiles[1:4],markers=1:25,beadInfo=beadInfo)
#Genotype calling
BSRed <- callGenotypes(BSRed)
genotypes <- translateTheta(assayData(BSRed)$call,fData(BSRed),type='regular')
print(cbind(fData(BSRed)$Classification,genotypes[,1:3])[1:10,])
#Alternative output
BSRed <- translateThetaCombined(BSRed)
print(cbind(fData(BSRed)$Classification,assayData(BSRed)$genotype[,1:3])[1:10,])