lcmsPlot-package	lcmsPlot-package
+,lcmsPlotClass,function-method	plus-lcmsPlotClass-function-method
.apply_options	dot-apply_options
.app_content	dot-app_content
.app_navrail	dot-app_navrail
.APP_TABS	dot-APP_TABS
.app_topbar	dot-app_topbar
.build_server	dot-build_server
.build_ui	dot-build_ui
.chromatogram_server	dot-chromatogram_server
.chromatogram_ui	dot-chromatogram_ui
.eic_features	dot-eic_features
.eic_server	dot-eic_server
.eic_ui	dot-eic_ui
.empty_to_null	dot-empty_to_null
.file_ext	dot-file_ext
.lcmsPlot_dep	dot-lcmsPlot_dep
.load_dataset	dot-load_dataset
.mz_window	dot-mz_window
.nav_active_js	dot-nav_active_js
.na_to_null	dot-na_to_null
.options_server	dot-options_server
.options_ui	dot-options_ui
.peak_density_server	dot-peak_density_server
.peak_density_ui	dot-peak_density_ui
.spectra_server	dot-spectra_server
.spectra_ui	dot-spectra_ui
.SUPPORTED_DATA_CLASSES	dot-SUPPORTED_DATA_CLASSES
.tic_server	dot-tic_server
.tic_ui	dot-tic_ui
.toast_error	dot-toast_error
.uploaded_files_to_paths	dot-uploaded_files_to_paths
convert_rt_to_seconds	convert_rt_to_seconds
create_bpc_tic	create_bpc_tic
create_chromatogram	create_chromatogram
create_chromatograms	create_chromatograms
create_chromatograms,ANY,data.frame,list,ANY-method	create_chromatograms
create_chromatograms,ANY,data.frame,list,character-method	create_chromatograms
create_chromatograms,ANY,data.frame,list,NULL-method	create_chromatograms
create_chromatograms,DBIConnection,data.frame,list,NULL-method	create_chromatograms
create_chromatograms,MChromatograms,data.frame,list,NULL-method	create_chromatograms
create_chromatograms,XChromatogram,data.frame,list,NULL-method	create_chromatograms
create_chromatograms,XChromatograms,data.frame,list,NULL-method	create_chromatograms
create_chromatograms,XcmsRawList,data.frame,list,ANY-method	create_chromatograms
create_chromatograms,XcmsRawList,data.frame,list,NULL-method	create_chromatograms
create_data_container_from_obj	create_data_container_from_obj
create_intensity_map	create_intensity_map
create_intensity_map,lcmsPlotDataContainer,list-method	create_intensity_map
create_isolation_window	create_isolation_window
create_peak_density	create_peak_density
create_peak_density,lcmsPlotDataContainer,list-method	create_peak_density
create_purity_scores	create_purity_scores
create_rt_diff	create_rt_diff
create_rt_diff,lcmsPlotDataContainer,list-method	create_rt_diff
create_spectra	create_spectra
create_spectra,lcmsPlotDataContainer,list-method	create_spectra
create_spectra_for_sample	create_spectra_for_sample
create_spectrum_from_closest_scan_to_rt	create_spectrum_from_closest_scan_to_rt
create_spectrum_from_scan_index	create_spectrum_from_scan_index
create_total_ion_current	create_total_ion_current
create_total_ion_current,lcmsPlotDataContainer,list-method	create_total_ion_current
create_xcms_raw_list	create_xcms_raw_list
default_options	default_options
detect_separator	detect_separator
ExternalDataSource-class	ExternalDataSource-class
field	field
get_adjusted_rts	get_adjusted_rts
get_detected_peaks	get_detected_peaks
get_detected_peaks.character	get_detected_peaks
get_detected_peaks.ExternalDataSource	get_detected_peaks
get_detected_peaks.MChromatograms	get_detected_peaks
get_detected_peaks.MsExperiment	get_detected_peaks
get_detected_peaks.purityA	get_detected_peaks
get_detected_peaks.XChromatogram	get_detected_peaks
get_detected_peaks.XChromatograms	get_detected_peaks
get_detected_peaks.XCMSnExp	get_detected_peaks
get_detected_peaks.XcmsRawList	get_detected_peaks
get_features	get_features
get_feature_data	get_feature_data
get_grouped_peaks	get_grouped_peaks
get_grouped_peaks.default	get_grouped_peaks
get_grouped_peaks.MsExperiment	get_grouped_peaks
get_grouped_peaks.purityA	get_grouped_peaks
get_grouped_peaks.XcmsExperiment	get_grouped_peaks
get_grouped_peaks.XCMSnExp	get_grouped_peaks
get_grouping_variables	get_grouping_variables
get_metadata	get_metadata
get_metadata.character	get_metadata
get_metadata.DBIConnection	get_metadata
get_metadata.ExternalDataSource	get_metadata
get_metadata.MChromatograms	get_metadata
get_metadata.MsExperiment	get_metadata
get_metadata.purityA	get_metadata
get_metadata.XChromatogram	get_metadata
get_metadata.XChromatograms	get_metadata
get_metadata.XCMSnExp	get_metadata
get_metadata.XcmsRawList	get_metadata
get_mz_range	get_mz_range
get_workflow_input_files	get_workflow_input_files
get_XCMSnExp_object_example	get_XCMSnExp_object_example
get_xic_traces_from_compounds	get_xic_traces_from_compounds
io_close_raw_data	io_close_raw_data
io_get_raw_data	io_get_raw_data
is_cd_result	is_cd_result
is_cd_results_path	is_cd_results_path
is_mspurity_data	is_mspurity_data
is_xcms_data	is_xcms_data
is_xcms_processed_data	is_xcms_processed_data
iterate_plot_batches	iterate_plot_batches
iterate_plot_batches,lcmsPlotClass,function-method	iterate_plot_batches
lcmsPlot	lcmsPlot
lcmsPlotApp	lcmsPlotApp
lcmsPlotClass-class	lcmsPlotClass-class
lcmsPlotDataContainer-class	lcmsPlotDataContainer-class
lp_arrange	lp_arrange
lp_chromatogram	lp_chromatogram
lp_compound_discoverer	lp_compound_discoverer
lp_facets	lp_facets
lp_get_plot	lp_get_plot
lp_grid	lp_grid
lp_intensity_map	lp_intensity_map
lp_isolation_window	lp_isolation_window
lp_labels	lp_labels
lp_layout	lp_layout
lp_legend	lp_legend
lp_mass_trace	lp_mass_trace
lp_peak_density	lp_peak_density
lp_purity_distribution	lp_purity_distribution
lp_purity_overlay	lp_purity_overlay
lp_purity_timeline	lp_purity_timeline
lp_rt_diff_plot	lp_rt_diff_plot
lp_rt_line	lp_rt_line
lp_spectra	lp_spectra
lp_total_ion_current	lp_total_ion_current
merge_by_index	merge_by_index
MsDialPeaksSource	MsDialPeaksSource
MsRawReader-class	MsRawReader-class
ms_chromatogram	ms_chromatogram
ms_chromatogram,MzrReader-method	ms_chromatogram
ms_chromatogram,RawrrReader-method	ms_chromatogram
ms_chromatogram,XcmsRawReader-method	ms_chromatogram
ms_close	ms_close
ms_close,MzrReader-method	ms_close
ms_close,RawrrReader-method	ms_close
ms_close,XcmsRawReader-method	ms_close
ms_header	ms_header
ms_header,MzrReader-method	ms_header
ms_header,RawrrReader-method	ms_header
ms_header,XcmsRawReader-method	ms_header
ms_peaks	ms_peaks
ms_peaks,MzrReader-method	ms_peaks
ms_peaks,RawrrReader-method	ms_peaks
ms_peaks,XcmsRawReader-method	ms_peaks
MZmineFeatureListsSource	MZmineFeatureListsSource
MzrReader-class	MzrReader-class
next_plot	next_plot
next_plot,lcmsPlotClass-method	next_plot
open_cd_result_connection	open_cd_result_connection
open_raw_reader	open_raw_reader
parse_trace	parse_trace
plot_chromatogram	plot_chromatogram
plot_data	plot_data
plot_intensity_map	plot_intensity_map
plot_isolation_window	plot_isolation_window
plot_mass_trace	plot_mass_trace
plot_multiple_datasets	plot_multiple_datasets
plot_multiple_faceted_datasets	plot_multiple_faceted_datasets
plot_peak_density	plot_peak_density
plot_purity_distribution	plot_purity_distribution
plot_purity_timeline	plot_purity_timeline
plot_rt_diff	plot_rt_diff
plot_single_dataset	plot_single_dataset
plot_spectrum	plot_spectrum
plot_total_ion_current	plot_total_ion_current
process_metadata	process_metadata
purity_overlay_layer	purity_overlay_layer
RawrrReader-class	RawrrReader-class
remove_null_elements	remove_null_elements
run_matching_plot_variant	run_matching_plot_variant
show,ExternalDataSource-method	show-ExternalDataSource-method
show,lcmsPlotClass-method	show-lcmsPlotClass-method
show,lcmsPlotDataContainer-method	show-lcmsPlotDataContainer-method
show,XcmsRawList-method	show-XcmsRawList-method
validate_data_frame	validate_data_frame
validate_object	validate_object
XcmsRawList	XcmsRawList
XcmsRawList-class	XcmsRawList-class
XcmsRawReader-class	XcmsRawReader-class
xcmsraw_to_readers	xcmsraw_to_readers
