writeAlleleSet: Write AlleleSetIllumina data to files
In beadarrayMSV: Analysis of Illumina BeadArray SNP data including MSV markers

Description Usage Arguments Details Value Warning Note Author(s) See Also Examples

View source: R/beadarrayMSV.R

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

1 2	writeAlleleSet(dataFiles, BSRed, append = TRUE, sep = "\t", 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

Use with caution, as files will be overwritten without question if so specified

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

Lars Gidskehaug

createAlleleSetFromFiles, makeFilenames, AlleleSetIllumina

## Not run: 
#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])

## End(Not run)