superFreq (version 1.2.3)

forceRedoNothing: returns input that uses saved data if present.

Description

returns input that uses saved data if present.

Usage

forceRedoNothing()

Details

This function returns the input 'forceRedo' for analyse(), so that saved data from previous runs is used if present. This should be the input normally.

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 = forceRedoNothing()
parameters = list('systematicVariance'=0.02, 'maxCov'=150)

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