BCL2FastQparams-class {basecallQC} | R Documentation |
Parameter class and accessors for use with basecallQC
Parameter class and accessors
BCL2FastQparams(runXML = NULL, config = NULL, runDir = NULL, outDir = NULL, verbose = TRUE)
runXML |
file path to runParameters.xml ,if not specified looks in top level of run directory. |
config |
file path to config.ini ,if not specified looks in top level of run directory. |
runDir |
file path to run directory. |
outDir |
file path to out directory. |
verbose |
TRUE or FALSE. Messages on or off. Warnings/errors persist |
The BCL2FastQparams object contains slots RunDir, OutDir and RunParameters
"RunDir" Character string specifying the top level Run directory
"OutDir" Character string specifying the output directory
"RunParameters" A data.frame containing the information from runParameters.xml (See vignette for more details).
A BCL2FastQparams object (See details).
fileLocations <- system.file("extdata",package="basecallQC") runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE) config <- dir(fileLocations,pattern="config.ini",full.names=TRUE) BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)