# Quick start guide

    # load isoorbi library
    library(isoorbi)

A basic data processing example

# Load

    # path to a test file included in the isoorbi package
    # this file contains data from multiple analyses for the same compound
    file_path <- system.file(package = "isoorbi", "extdata", "testfile_flow.isox")

    # load data
    df <-
      file_path |>
      # reads .isox test data
      orbi_read_isox() |>
      # optionally: keeps only most important columns; equivalent to simplify check box in IsoX
      orbi_simplify_isox()

    # If you wish to read a whole folder of files, you can use the orbi_find_isox() function
    # df <- "path_to_your_folder" |> orbi_find_isox() |> orbi_read_isox()

# Check

Now that the data is loaded, check for satellite peaks, weak isotopocules and outliers.

    # check for noise and outliers
    df_flagged <- df |>
      orbi_flag_satellite_peaks() |> # removes minor signals that were reported by IsoX in the same tolerance window where the peak of interest is
      orbi_flag_weak_isotopocules(min_percent = 2) |> # removes signals of isotopocules that were not detected at least in min_percent scans
      orbi_flag_outliers(agc_fold_cutoff = 2) # removes outlying scans that have more than 2 times or less than 1/2 times the average number of ions in the Orbitrap analyzer; another method: agc_window (see function documentation for more details)

The info messages from these functions suggest that no data was flagged.

# Calculate

    # define base peak and calculate the results table
    df_results <-
      df_flagged |>
      orbi_define_basepeak(basepeak_def = "M0")|> # sets one isotopocule in the dataset as the base peak (denominator) for ratio calculation
      orbi_summarize_results(ratio_method = "sum") # calculates ratios and generates a results table

# Visualize

    # use a ggplot to plot the data
    library(ggplot2)
    df_results |>
      ggplot() +
      aes(
        x = sprintf("%s/%s", isotopocule, basepeak),
        y = ratio, ymin = ratio - ratio_sem, ymax = ratio + ratio_sem,
        color = filename
      ) +
      geom_pointrange() +
      scale_color_brewer(palette = "Set1") +
      orbi_default_theme() +
      labs(x = NULL, y = "ratio") +
      facet_wrap(~compound)