writeAlleleSet: Write AlleleSetIllumina data to files

In beadarrayMSV: Analysis of Illumina BeadArray SNP data including MSV markers

Description

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

Usage

writeAlleleSet(dataFiles, BSRed, append = TRUE, sep = "\t",
    quote = FALSE)

Arguments

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)

Details

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.

Value

This function is used for its side effects

Warning

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

Note

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

Author(s)

Lars Gidskehaug

See Also

createAlleleSetFromFiles, makeFilenames, AlleleSetIllumina

Examples

## 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)

beadarrayMSV documentation built on May 29, 2017, 9:07 a.m.