Process Orbitrap Isotopocule Data

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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