# Process Orbitrap Isotopocule Data

## Documentation for package ‘isoorbi’ version 1.5.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

isoorbi-package | isoorbi: Process Orbitrap Isotopocule Data
get_pkg_options | Package options
isoorbi | isoorbi: Process Orbitrap Isotopocule Data
orbi_add_blocks_to_plot | Plot blocks background
orbi_add_to_aggregator | Dynamic data agreggator
orbi_adjust_block | Manually adjust block delimiters
orbi_aggregate_raw | Aggregate data from raw files
orbi_analyze_shot_noise | Shot noise calculation
orbi_calculate_ions | Calculate ions from intensities
orbi_calculate_ratios | Calculate direct isotopocule ratios
orbi_calculate_summarized_ratio | Calculate isotopocule ratio
orbi_check_isoraw | Check for the isoorbi raw file reader
orbi_default_theme | Default isoorbi plotting theme
orbi_define_basepeak | Define the denominator for ratio calculation
orbi_define_blocks_for_dual_inlet | Binning raw data into blocks for dual inlet analyses
orbi_define_block_for_flow_injection | Define data block for flow injection
orbi_export_data_to_excel | Export data to excel
orbi_filter_files | Basic generic data files filter
orbi_filter_flagged_data | Filter out flagged data
orbi_filter_isotopocules | Filter isotopocules
orbi_filter_isox | Filter isox files
orbi_filter_satellite_peaks | Function replaced by 'orbi_flag_satellite_peaks()'
orbi_filter_scan_intensity | Function replaced by 'orbi_flag_outliers()'
orbi_filter_weak_isotopocules | Function replaced by 'orbi_flag_weak_isotopocules()'
orbi_find_isox | Find isox files
orbi_find_raw | Find raw files
orbi_flag_outliers | Flag outlier scans
orbi_flag_satellite_peaks | Flag minor satellite peaks Flags minor signals for an isotopocule that matches multiple peaks within its exact mass +/- tolerance interval in the same scan. These are often small satellite peaks generated by the Fourier transform. However, if there are satelite peaks of high intensity or very many satellite peaks, it can indicate that the m/z and tolerance setting used for identifying isotopcules need to be revisited. Visualize the flagged satellite peaks with 'orbi_plot_satellite_peaks()'.
orbi_flag_weak_isotopocules | Flag weak isotopocules
orbi_get_aggregator | Dynamic data agreggator
orbi_get_blocks_info | Summarize blocks info
orbi_get_data | Get data frame from aggregated data
orbi_get_example_files | Get available example file(s)
orbi_get_isotopocule_coverage | Isotopocule coverage
orbi_get_option | Package options
orbi_get_options | Package options
orbi_get_problems | Retrieve parsing problems
orbi_get_settings | Get all isoorbi package settings
orbi_identify_isotopocules | Identify isotopocules
orbi_options | Package options
orbi_plot_isotopocule_coverage | Isotopocule coverage
orbi_plot_raw_data | Visualize data
orbi_plot_satellite_peaks | Visualize satellite peaks
orbi_plot_shot_noise | Make a shot noise plot
orbi_plot_spectra | Plot mass spectra
orbi_read_isox | Read IsoX file
orbi_read_raw | Read RAW files
orbi_register_aggregator | Dynamic data agreggator
orbi_segment_blocks | Segment data blocks
orbi_set_settings | Set package settings
orbi_show_problems | Retrieve parsing problems
orbi_simplify_isox | Simplify IsoX data
orbi_start_aggregator | Dynamic data agreggator
orbi_summarize_results | Generate the results table