## ----echo = FALSE, message = FALSE, warning = FALSE--------------------------- knitr::opts_chunk$set(collapse = TRUE, comment = "#>") library(faahKO) ## ----install_IPO, eval=FALSE-------------------------------------------------- # # try http:// if https:// URLs are not supported # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("IPO") ## ----install_IPO_suggestions, eval=FALSE-------------------------------------- # # for examples of peak picking parameter optimization: # BiocManager::install("msdata") # # for examples of optimization of retention time correction and grouping # # parameters: # BiocManager::install("faahKO") ## ----file_choosing------------------------------------------------------------ datapath <- system.file("cdf", package = "faahKO") datafiles <- list.files(datapath, recursive = TRUE, full.names = TRUE) ## ----load_IPO, message=FALSE-------------------------------------------------- library(IPO) ## ----optimize_peak_picking, fig.height=7, fig.width=7, warning=FALSE---------- peakpickingParameters <- getDefaultXcmsSetStartingParams('matchedFilter') #setting levels for step to 0.2 and 0.3 (hence 0.25 is the center point) peakpickingParameters$step <- c(0.2, 0.3) peakpickingParameters$fwhm <- c(40, 50) #setting only one value for steps therefore this parameter is not optimized peakpickingParameters$steps <- 2 time.xcmsSet <- system.time({ # measuring time resultPeakpicking <- optimizeXcmsSet(files = datafiles[1:2], params = peakpickingParameters, nSlaves = 1, subdir = NULL, plot = TRUE) }) ## ----optimize_peak_picking_result--------------------------------------------- resultPeakpicking$best_settings$result optimizedXcmsSetObject <- resultPeakpicking$best_settings$xset ## ----optimize_retcor_group, fig.height=7, fig.width=7, warning = FALSE-------- retcorGroupParameters <- getDefaultRetGroupStartingParams() retcorGroupParameters$profStep <- 1 retcorGroupParameters$gapExtend <- 2.7 time.RetGroup <- system.time({ # measuring time resultRetcorGroup <- optimizeRetGroup(xset = optimizedXcmsSetObject, params = retcorGroupParameters, nSlaves = 1, subdir = NULL, plot = TRUE) }) ## ----display_settings--------------------------------------------------------- writeRScript(resultPeakpicking$best_settings$parameters, resultRetcorGroup$best_settings) ## ----times-------------------------------------------------------------------- time.xcmsSet # time for optimizing peak picking parameters time.RetGroup # time for optimizing retention time correction and grouping parameters sessionInfo()