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_aggregate_raw(): Aggregate data from raw files

orbi_start_aggregator() orbi_add_aggregator(): Dynamic data agreggator

orbi_get_data(): Get data frame from aggregated data

orbi_get_problems(): Retrieve parsing problems

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 proessing functions

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

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_isox(): Basic generic filter for IsoX data

orbi_flag_outliers(): Flag outlier scans

orbi_flag_satellite_peaks(): Flag minor satellite peaks

orbi_flag_weak_isotopocules(): Flag weak isotopocules

orbi_get_isotopocule_coverage(): Calculate isotopocule coverage

Visualize data

These functions help visualize what happens to the data during processing

orbi_plot_satellite_peaks(): Visualize satellite peaks

orbi_plot_isotopocule_coverage(): Plot isotopocule coverage

orbi_plot_raw_data(): Visualize raw 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 frame 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_calculate_ratios(): Calculate direct isotopocule ratios

orbi_get_settings() deprecated: Get all isoorbi package settings

orbi_set_settings() deprecated: Set package settings