## ----eval=FALSE--------------------------------------------------------------- # #ensure you have mzR installed # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("mzR", version = "3.8") # # # install the package directly from Github # library(devtools) # devtools::install_github("JosieLHayes/adductomicsR") # # #install the data package containing the data # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("ExperimentHub", version = "3.9") # # #or download the packages and install from source # library(devtools) # devtools::install("path_to_dir/adductomicsR") # devtools::install("path_to_dir/adductData") # ## ----eval=FALSE--------------------------------------------------------------- # # load the package # library(adductomicsR) # library(adductData) # library(ExperimentHub) ## ----echo=FALSE--------------------------------------------------------------- suppressMessages(suppressWarnings(library(adductomicsR))) suppressMessages(suppressWarnings(library(ExperimentHub))) ## ----quiet=TRUE, error = TRUE------------------------------------------------- eh = suppressMessages(suppressWarnings(ExperimentHub::ExperimentHub())) temp = suppressMessages(suppressWarnings( AnnotationHub::query(eh, 'adductData'))) ## ----quiet=TRUE, error = TRUE------------------------------------------------- suppressMessages(suppressWarnings(temp[['EH1957']])) #first mzXML file file.rename(cache(temp["EH1957"]), file.path(hubCache(temp), 'ORB35017.mzXML')) temp[['EH1958']] #second mzXML file file.rename(cache(temp["EH1958"]), file.path(hubCache(temp), 'ORB35022.mzXML')) ## ----quiet=TRUE, eval=FALSE--------------------------------------------------- # rtDevModelling( # MS2Dir = hubCache(temp), # nCores=4, # runOrder =paste0(system.file("extdata", # package ="adductomicsR"),'/runOrder.csv') # ) ## ----quiet=TRUE, eval=FALSE--------------------------------------------------- # specSimPepId( # MS2Dir = hubCache(temp), # nCores=4, # rtDevModels =paste0(hubCache(temp),'/rtDevModels.RData') # ) ## ----quiet=TRUE, error=TRUE--------------------------------------------------- generateTargTable( allresultsFile=paste0(system.file("extdata",package = "adductomicsR"),'/allResults_ALVLIAFAQYLQQCPFEDHVK_example.csv'), csvDir=tempdir(check = FALSE) ) ## ----quiet=TRUE, eval=FALSE--------------------------------------------------- # adductQuant( # nCores=2, # targTable=paste0(system.file("extdata", # package="adductomicsR"), # '/exampletargTable2.csv'), # intStdRtDrift=30, # rtDevModels= paste0(hubCache(temp),'/rtDevModels.RData'), # filePaths=list.files(hubCache(temp),pattern=".mzXML", # all.files=FALSE,full.names=TRUE), # quantObject=NULL, # indivAdduct=NULL, # maxPpm=5, # minSimScore=0.8, # spikeScans=1, # minPeakHeight=100, # maxRtDrift=20, # maxRtWindow=240, # isoWindow=80, # hkPeptide='LVNEVTEFAK', # gaussAlpha=16 # ) # ## ----quiet=TRUE, eval=FALSE, error=TRUE--------------------------------------- # #load the adductquantif object # load(paste0(hubCache(temp),"/adductQuantResults.Rda")) # # #produce a peakTable from the Adductquantif object and save to a temporary # #directory # suppressMessages(suppressWarnings(outputPeakTable(object= # object, outputDir=tempdir(check = FALSE)))) ## ----quiet=TRUE,eval=FALSE, error=TRUE---------------------------------------- # filterAdductTable( # paste0(tempdir(check = FALSE),"/adductQuantif_peakList_", Sys.Date(), ".csv") # ) ## ----quiet=TRUE, error=TRUE--------------------------------------------------- #session info sessionInfo()