writeAlleleSet: Write AlleleSetIllumina data to files

Description

Writes assayData, phenoData, and/or featureData of "AlleleSetIllumina" objects to text-files
Usage

writeAlleleSet(dataFiles, BSRed, append = TRUE, sep = "",
    quote = FALSE)
dataFiles{
    List with file-names (see makeFilenames). Only
    elements of BSRed indicated here are saved
  }
  BSRed{
    "AlleleSetIllumina" object
  }
  append{
    If TRUE, append data rather than overwrite files (see write.table)
  }
  sep{
    Field delimiter string (see write.table)
  }
  quote{
    If TRUE, character and factor columns are quoted (see write.table)
  }
The data-tables specified is written to text-files for subsequent
  loading using
  createAlleleSetFromFiles
  (or similar). The pre-processed data-files intFile,
  thFile, seFile, and phFile are used to estimate the
  result-files callFile, resFile, and
  genoFile. Subsequent overwriting of data-files may therefore
  invalidate result-file. Therefore, no data-files will be
  saved if result-files are saved in the same run.
This function is used for its side effects
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]
The assayData-entries intensity, theta, and
  SE are written array-wise to file. This enables
  pre-processing of a subset of arrays at the time. The entries
  call and genotype are written marker-wise, which
  enables genotype-calling of a subset of markers at the time
Warning{
  Use with caution, as files will be overwritten without question if so specified
}
createAlleleSetFromFiles, makeFilenames,
  AlleleSetIllumina
#Create an AlleleSetIllumina object using files in example data directory
rPath <- system.file("extdata", package="beadarrayMSV")
normOpts <- list(transf='root',method='medianAF')
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],beadInfo=beadInfo)
#Write some data to files
writeFiles <- makeFilenames('test2',normOpts,path='.')
writeAlleleSet(writeFiles[1:4],BSRed[1:10,1:5])
Description

Usage

Arguments
