makeFilenames: Generate filenames reflecting normalizations

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

View source: R/beadarrayMSV.R

Description

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

Usage

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

modifyExistingFilenames(dataFiles, oldtag, newtag)

Arguments

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.

Details

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.

Value

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

Warning

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)

Author(s)

Lars Gidskehaug

See Also

writeAlleleSet, createAlleleSetFromFiles, createMultiSetFromFiles, translateThetaFromFiles

Examples

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#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')

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