## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) library(readxl) ## ----echo=FALSE, eval=TRUE, message=FALSE------------------------------------- # not nice, but we need the IsoCorrectoR data to generate to tool_features table ! # load package library(IsoCorrectoR) # load IsoCorrectoR example data data(IsoCorrectoR) ## ----toolFeaturesTable, echo=FALSE, eval=TRUE--------------------------------- knitr::kable( IsoCorrectoR$tool_features ) ## ----echo=TRUE, eval=FALSE---------------------------------------------------- # IsoCorrection(MeasurementFile=NA, ElementFile=NA, MoleculeFile=NA, # CorrectTracerImpurity=FALSE, CorrectTracerElementCore=TRUE, # CalculateMeanEnrichment=TRUE, UltraHighRes=FALSE, # DirOut='.', FileOut='result', FileOutFormat='csv', # ReturnResultsObject=FALSE, CorrectAlsoMonoisotopic=FALSE, # CalculationThreshold=10^-8, CalculationThreshold_UHR=8, # verbose=FALSE, Testmode=FALSE) ## ----moleculeFileExampleNormalRes, echo=FALSE, eval=TRUE---------------------- fileExample <- IsoCorrectoR[["normal_resolution"]][["molecule_file"]] fileExample[4:7, 3] <- "" knitr::kable( fileExample, align = "l", caption="Molecule information for normal resolution data" ) ## ----moleculeFileExampleHighRes, echo=FALSE, eval=TRUE------------------------ fileExample <- IsoCorrectoR[["high_resolution"]][["molecule_file"]] fileExample[is.na(fileExample)] <- "" knitr::kable( fileExample, align = "l", caption="Molecule information for high resolution data" ) ## ----measurementFileExampleNormRes, echo=FALSE, eval=TRUE--------------------- fileExample <- IsoCorrectoR[["normal_resolution"]][["measurement_file"]] #Subset and adjust example to illustrate explanations fileExample <- fileExample[c(1:6, 40:43),1:6] fileExample[7:10,1] <- gsub('.{2}$', '', fileExample[7:10,1]) fileExample[c(4,6), "Sample3"] <- "" fileExample[4, "Sample5"] <- "" fileExample[9, "Sample1"] <- "" knitr::kable( fileExample, align = "l", row.names = FALSE, caption="Measurement information for normal resolution data" ) ## ----measurementFileExampleHighRes, echo=FALSE, eval=TRUE--------------------- fileExample <- IsoCorrectoR[["high_resolution"]][["measurement_file"]] #Subset and adjust example to illustrate explanations fileExample <- fileExample[1:21,1:6] fileExample[20,"Sample3"] <- "" fileExample[21,"Sample3"] <- "0" fileExample[16,"Sample3"] <- "" knitr::kable( fileExample, align = "l", row.names = FALSE, caption="Measurement information for high resolution data" ) ## ----elementFileExample, echo=FALSE, eval=TRUE-------------------------------- fileExample <- IsoCorrectoR$element_file fileExample[is.na(fileExample)] <- "" knitr::kable( fileExample, align = "l", caption="Element information (resolution independent)" ) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()