isoorbi

Overview

Installation

# install the isoorbi packageinstall.packages("isoorbi")# check/install the isoraw readerisoorbi::orbi_check_isoraw()

Development version

# checks that you are set up to build R packages from sourceif (!requireNamespace("pkgbuild",quietly=TRUE)) {  install.packages("pkgbuild")}pkgbuild::check_build_tools()# installs the latest isoorbi package from GitHubif (!requireNamespace("pak",quietly=TRUE)) {  install.packages("pak")}pak::pak("isoverse/isoorbi")# check/install the isoraw readerisoorbi::orbi_check_isoraw()

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Read raw data file

# load librarylibrary(isoorbi)# provide the path to your data folder here:my_data_folder<- file.path("project","data")# and search for raw files in that folderfile_paths<- orbi_find_raw(my_data_folder)# for this example, we use a small raw test file bundled with the# package instead (remove this line if working with your own data)file_paths<- orbi_get_example_files("nitrate_test_10scans.raw")# read the raw file incluing 2 of the raw spectraraw_files<-file_paths|>  orbi_read_raw(include_spectra= c(1,10))# aggregate the raw data (processes the read files)raw_agg<-raw_files|> orbi_aggregate_raw()# plot the spectraraw_agg|> orbi_plot_spectra()

Identify isotopcules

# identify isotopcules# these could also come from a data frame or a tsv/csv/excel fileraw_agg<-raw_agg|>  orbi_identify_isotopocules(isotopocules= c("M0"=61.9878,"15N"=62.9850,"17O"=62.9922,"18O"=63.9922    )  )# plot again, now with the isotopocules identifiedraw_agg|> orbi_plot_spectra()

Process data

# process raw files datadataset<-raw_agg|># check for satellite peaks  orbi_flag_satellite_peaks()|># filter out unidentified isotopocules# (happes automatically during define_basepeak as of version 1.5.3)  orbi_filter_isotopocules()|># define base peak  orbi_define_basepeak(basepeak_def="M0")# plot the resulting isotopocule ratiosdataset|> orbi_plot_raw_data(y=ratio)

Summarize results

# calculate ratios across scansresults<-dataset|> orbi_summarize_results(ratio_method="sum")# print resultsresults|> orbi_get_data(summary= c("isotopocule","ratio","ratio_sem"))# export results to excelresults|>  orbi_export_data_to_excel(file="data_summary.xlsx",# note: as of version 1.5.3, this is the default and does not need to# be specified explicitly anymoreinclude= c("file_info","summary")  )

Package structure

Getting help

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