makeFilenames: Generate filenames reflecting normalizations
In beadarrayMSV: Analysis of Illumina BeadArray SNP data including MSV markers

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

Filenames including paths are generated to enable writing a set of "AlleleSetIllumina" data-tables to text-files. These are used subsequently to read specified markers and arrays into the workspace

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makeFilenames(tag, normOpts, path = ".")

modifyExistingFilenames(dataFiles, oldtag, newtag)

`tag`	Character string included in the filenames which is unique to the current analysis
`normOpts`	List with pre-processing options used (see `setNormOptions`). Generated filnames will reflect the transformation and channel-normalisation performed on the data
`path`	Character string with the saving path
`dataFiles`	Character vector with previous output from `makeFilenames`
`oldtag`	Often several rounds of genotype-calling is performed based on the same, pre-processed data. This character string correspond to the unique tag used for the previous run(s).
`newtag`	A new character string tag to replace `oldtag` in files other than those pre-processed data-files which remain the same between runs.

These files generate file names used for reading and writing between text files and workspace. When different runs of genotype calling is performed using the same, pre-processed data, modifyExistingFilenames updates only the elements which change with the new genotyping.

Character vector with the fields

`intFile`	File name for `intensity` values
`thFile`	File name for `theta` values
`seFile`	File name for `SE` values
`phFile`	File name for phenotype data
`callFile`	File name for `call` values
`resFile`	File name for feature data such as call statistics
`genoFile`	File name for `allele` values

Warnings are issued if existing filenames are used, as this may lead to overwriting of these files in subsequent steps (no files are overwritten by the functions themselves)

Lars Gidskehaug

writeAlleleSet, createAlleleSetFromFiles, createMultiSetFromFiles, translateThetaFromFiles

#Create names
normOpts <- setNormOptions()
tag <- '1'
dataFiles <- makeFilenames(tag,normOpts)
print(dataFiles)

#Make new names for subsequent, alternate genotype calling runs
dataFiles <- modifyExistingFilenames(dataFiles,tag,'2')