Package index • isoorbi

Read RAW files

These functions allow reading of raw files directly

orbi_find_raw(): Find raw files

orbi_read_raw(): Read RAW files

orbi_check_isoraw(): Check for the isoorbi raw file reader

orbi_get_problems() orbi_show_problems(): Retrieve parsing problems

orbi_get_example_files(): Get available example file(s)

Aggregate RAW files data

These functions extract data from raw files

orbi_aggregate_raw(): Aggregate data from raw files

orbi_start_aggregator() orbi_add_to_aggregator() orbi_register_aggregator() orbi_get_aggregator(): Dynamic data agreggator

orbi_get_data(): Get data frame from aggregated data

Read ISOX files

These functions allow reading of isox files

orbi_find_isox(): Find isox files

orbi_read_isox(): Read IsoX file

orbi_simplify_isox(): Simplify IsoX data

Core processing functions

These core functions are essential to process the data read from RAW or ISOX files

orbi_identify_isotopocules(): Identify isotopocules

orbi_calculate_ions(): Calculate ions from intensities

orbi_define_basepeak(): Define the denominator for ratio calculation

orbi_summarize_results(): Generate the results table

orbi_calculate_summarized_ratio(): Calculate isotopocule ratio

Define data blocks

These functions are useful for annotating and processing dual inlet and flow injection data.

orbi_define_block_for_flow_injection(): Define data block for flow injection

orbi_define_blocks_for_dual_inlet(): Binning raw data into blocks for dual inlet analyses

orbi_adjust_block(): Manually adjust block delimiters

orbi_segment_blocks(): Segment data blocks

orbi_get_blocks_info(): Summarize blocks info

Curate data

These functions handle data selection and flagging outliers.

orbi_filter_isotopocules(): Filter isotopocules

orbi_filter_files(): Basic generic data files filter

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_plot_isotopocule_coverage() orbi_get_isotopocule_coverage(): Isotopocule coverage

Visualize data

These functions help visualize what happens to the data during processing

orbi_plot_spectra(): Plot mass spectra

orbi_plot_satellite_peaks(): Visualize satellite peaks

orbi_plot_isotopocule_coverage() orbi_get_isotopocule_coverage(): Isotopocule coverage

orbi_plot_raw_data(): Visualize data

orbi_add_blocks_to_plot(): Plot blocks background

orbi_default_theme(): Default isoorbi plotting theme

Shot noise analysis

These functions are available for analysis of shot noise in collected data and creating shot noise plots.

orbi_analyze_shot_noise(): Shot noise calculation

orbi_plot_shot_noise(): Make a shot noise plot

Export functions

This function serves to export data to an Excel file.

orbi_export_data_to_excel(): Export data to excel

Package options

These functions are available to simplify or customize the data analysis.

isoorbi isoorbi-package: isoorbi: Process Orbitrap Isotopocule Data

orbi_options() orbi_get_options() orbi_get_option(): Package options

Deprecated functions

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_filter_flagged_data(): Filter out flagged data

orbi_filter_isox() deprecated: Filter isox files

orbi_calculate_ratios(): Calculate direct isotopocule ratios

orbi_get_settings() deprecated: Get all isoorbi package settings

orbi_set_settings() deprecated: Set package settings