## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----installDIAlignR, eval=FALSE---------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("DIAlignR") ## ----loadDIAlignR------------------------------------------------------------- library(DIAlignR) ## ----getDataPath-------------------------------------------------------------- dataPath <- system.file("extdata", package = "DIAlignR") ## ----results=FALSE, message=FALSE, warning=FALSE------------------------------ runs <- c("hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt", "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt") params <- paramsDIAlignR() params[["context"]] <- "experiment-wide" ## ----results=FALSE, message=FALSE, warning=FALSE------------------------------ # For specific runs provide their names. alignTargetedRuns(dataPath = dataPath, outFile = "test", runs = runs, oswMerged = TRUE, params = params) # For all the analytes in all runs, keep them as NULL. alignTargetedRuns(dataPath = dataPath, outFile = "test", runs = NULL, oswMerged = TRUE, params = params) ## ----results=FALSE, message=FALSE, warning=FALSE------------------------------ tree <- "run2 run2\nrun1 run0" mstAlignRuns(dataPath = dataPath, outFile = "test", mstNet = tree, oswMerged = TRUE, params = params) # Compute tree on-the-fly mstAlignRuns(dataPath = dataPath, outFile = "test", oswMerged = TRUE, params = params) ## ----results=FALSE, message=FALSE, warning=FALSE------------------------------ text1 <- "(run1:0.08857142857,(run0:0.06857142857,run2:0.06857142857)masterB:0.02)master1;" progAlignRuns(dataPath = dataPath, outFile = "test", newickTree = text1, oswMerged = TRUE, params = params) # Compute tree on-the-fly progAlignRuns(dataPath = dataPath, outFile = "test", oswMerged = TRUE, params = params) ## ----message=FALSE------------------------------------------------------------ runs <- c("hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt", "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt") AlignObjLight <- getAlignObjs(analytes = 4618L, runs = runs, dataPath = dataPath, objType = "light", params = params) # First element contains names of runs, spectra files, chromatogram files and feature files. AlignObjLight[[1]][, c("runName", "spectraFile")] obj <- AlignObjLight[[2]][["4618"]][[1]][["AlignObj"]] slotNames(obj) names(as.list(obj)) AlignObjMedium <- getAlignObjs(analytes = 4618L, runs = runs, dataPath = dataPath, objType = "medium", params = params) obj <- AlignObjMedium[[2]][["4618"]][[1]][["AlignObj"]] slotNames(obj) ## ----fig.width=6, fig.align='center', fig.height=6, message=FALSE------------- runs <- c("hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt", "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt") AlignObj <- getAlignObjs(analytes = 4618L, runs = runs, dataPath = dataPath, params = params) plotAlignedAnalytes(AlignObj, annotatePeak = TRUE) ## ----fig.width=5, fig.align='center', fig.height=5, message=FALSE------------- library(lattice) runs <- c("hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt", "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt") AlignObjOutput <- getAlignObjs(analytes = 4618L, runs = runs, params = params, dataPath = dataPath, objType = "medium") plotAlignmentPath(AlignObjOutput) ## ----------------------------------------------------------------------------- sessionInfo()