Description Usage Arguments Details Value Warning Note Author(s) See Also Examples
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 |
BSRed |
|
append |
If |
sep |
Field delimiter string (see |
quote |
If |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## 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)
|
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