ParserParams {WMBrukerParser}R Documentation

Input Parameter List

Description

ParserParams is a list of seven parameters which identify the data to be parsed, and specify whether or not data from multiple bioprocessor runs are to be concatenated and if memory use information is to be printed during parsing. For convenience, it is stored in a file named OptionsAndParameters.txt file which can be edited and sourced prior to execution of ParseAndSave.

Format

ParserParams$dataSource : character string (e.g. “Lab1”)
ParserParams$multipleRuns : character string (“yes” or “no” )
ParserParams$concatLists : character string (“yes” or “no” )
ParserParams$runIndices : numeric array (e.g. 1 or c(1,3,2) )
ParserParams$dataDirLeft : character string (e.g. “scr/MyRun”)
ParserParams$dataDirRight : character string (e.g. “QC”)
ParserParams$printMemoryUse: character string (“yes” or “no” )

Details

Data directories contain the spot directories with names such as 0_A1 or 0_B17. ParserParams$dataDirLeft, ParserParams$runIndices and ParserParams$dataDirRight are defined so that pasting them together generates the data directory paths desired. If multiple runs are to be parsed, the ParserParams$runIndices need not be in order but must appear in the paths. The "run branch" can occur at the level of the data directory or above. If it occurs at the data directory level,ParserParams$dataDirRight <- "". If a single run is to be parsed, ParserParams$dataDirLeft is assigned the complete data directory path, ParserParams$runIndices <- 1 and ParserParams$dataDirRight <- "".

See Also

WMBrukerParser, BrukerParser, ParserParams, ParseAndSave, tofListMetaData

Examples

## Example1: Parse data from a single bioprocessor run:

ParserParams<-list()
ParserParams$dataSource <- "Lab1"
ParserParams$multipleRuns <- "no" 
ParserParams$concatLists <- "no" 
ParserParams$runIndices <- 1

directory = system.file("Examples", package = "WMBrukerParser")
ParserParams$dataDirLeft <- 
paste(directory,"/C3ValidationExtractSmall/RobotRun1/2-100kDa",sep="")

ParserParams$dataDirRight <- "" 
ParserParams$printMemoryUse <- "no"

ParseAndSave(ParserParams)

## Example2: Parse and concatenate data from two bioprocessor
## two runs with memory information printed:

ParserParams<-list()
ParserParams$dataSource <- "Lab1"
ParserParams$multipleRuns <- "yes" 
ParserParams$concatLists <- "yes" 
ParserParams$runIndices <- c(1,2)

directory = system.file("Examples", package = "WMBrukerParser")
ParserParams$dataDirLeft <- 
paste(directory,"/C3ValidationExtractSmall/RobotRun",sep="")

ParserParams$dataDirRight <- "/2-100kDa" 
ParserParams$printMemoryUse <- "yes"

ParseAndSave(ParserParams)


[Package WMBrukerParser version 1.1 Index]