superFreq (version 1.2.3)

forceRedoEverything: returns input that uses saved data if present.

Description

returns input that uses saved data if present.

Usage

forceRedoEverything()

Details

This function returns the input 'forceRedo' for analyse(), so that all the analysis is redone, overwriting previously saved data exists.

Examples

# NOT RUN {
cpus=4
metaDataFile = '/absolute/path/to/myAnalysis/metaData.txt'
vcfFiles = list.files('/absolute/path/to/myAnalysis/vcf', pattern='chr[0-9XYMT]+.vcf$', full.names=T)
captureRegionsFile = '/absolute/path/to/myAnalysis/captureRegions.gc.bed'
dbSNPdirectory = '/absolute/path/to/myAnalysis/dbSNP'
normalDirectory = '/absolute/path/to/myAnalysis/normal'
Rdirectory = '/absolute/path/to/myAnalysis/R/'
plotDirectory = '/absolute/path/to/myAnalysis/plots/'

#The base quality phred offset. This can be read from fastqc analysis for example.
BQoffset = 33
genome = 'hg19'

inputFiles = list('metaDataFile'=metaDataFile, 'vcfFiles'=vcfFiles, 'normalDirectory'=normalDirectory,
'captureRegionsFile'=captureRegionsFile, 'dbSNPdirectory'=dbSNPdirectory)
outputDirectories = list('Rdirectory'=Rdirectory, 'plotDirectory'=plotDirectory)
runtimeSettings = list('cpus'=cpus, 'outputToTerminalAsWell'=T)

forceRedo = forceRedoEverything()
parameters = list('systematicVariance'=0.02, 'maxCov'=150)

data = analyse(inputFiles, outputDirectories, settings, forceRedo, runtimeSettings, parameters=parameters)
# }