A basic data processing example
# Path to a test file included in the isoorbi pacakge
file_path <- system.file(package = "isoorbi", "extdata", "testfile_flow.isox")
# Read .isox test data
df <- file_path |> orbi_read_isox()
# Keep only most important columns; equivalent to simplify check box in IsoX
df.simple <- df |> orbi_simplify_isox()
# Filter the data
df.filtered <- df.simple |>
orbi_filter_isox(
time_min = 0,
time_max = 1,
compounds = "HSO4-",
isotopocules = c("M0", "34S", "18O")
)
# Clean the data by removing noise and outliers
df.clean <- df.filtered |>
orbi_flag_satellite_peaks() |>
orbi_flag_weak_isotopocules(min_percent = 2) |>
orbi_flag_outliers(intensity_window = c(1,99))
# Define base peak and calculate the results table
df.results <- df.clean |>
orbi_define_basepeak(basepeak_def = "M0")|>
orbi_summarize_results(ratio_method = "sum")