Package index • TRACE

All functions

get_PAVE_from_MSdev(): PAVE analysis
TRACE_CN_labelling_ratio_adjust(): Adjust CN labelling ratio and optionally reconstruct CN hits
TRACE_LowC_cutoff: TRACE low-C cutoff table
TRACE_annotate(): Annotate TRACE seed network candidates and finalize TRACE result
TRACE_cache_all_network_split_demos(): Export all network split demos to cache
TRACE_cache_network_split_demo(): Build and cache a TRACE CN network split demo
TRACE_dynamic_filter(): Apply dynamic m/z and RT filtering for TRACE network
TRACE_export(): Export TRACE results to xlsx
TRACE_get_CN_net(): Build initial TRACE CN/adduct/isotope/fragment candidate networks
TRACE_load_network_split_demo(): Load a cached TRACE network split demo
TRACE_network_assignment(): Build TRACE seed network assignment
TRACE_score_mat_component(): Recompute path-compatibility score matrix for one component
TRACE_workflow(): Run the refactored TRACE workflow
build_instrument_parameter_table(): Build wide instrument-parameter table for PAVE2 datasets
build_instrument_ratio_shift_data(): Build ratio-shift data from multi-instrument PAVE2 files
compare_pave_adduct_conflict_demos(): Ranked adduct-conflict demos: PAVE adduct -> adduct -> ... -> metabolite
compare_pave_adduct_data(): Build PAVE vs TRACE adduct selection comparison data
compare_pave_adduct_distribution(): Adduct type counts for PAVE and TRACE barplots
compare_pave_cn_bundle_data(): Build PAVE vs TRACE CN bundle comparison data
compare_pave_dyn_filtered_xic_data(): Dynamic-filter vs overlap CN seed metadata for XIC comparison
compare_pave_fragment_data(): Build PAVE fragment vs TRACE annotation comparison data
compare_pave_lib_assignment_error_data(): CN bundle max errors for manual library-assignment types
compare_pave_lib_miss_detail(): Per-feature library mismatch diagnosis (PAVE-only and TRACE-only)
compare_pave_trace_diff_metabolite_data(): Build PAVE vs TRACE metabolite assignment table for manual review
compare_pave_wrong_cn_pave_demos(): Select wrong-CN demos from an assignment table
compute_TRACE_network_layout(): Compute fixed node coordinates for comparable network plots
compute_absorb_forms(): Calculate absorb-form fractions per sample
drop_absorb_c0n0(): Drop fully labeled absorb form C0N0
export_compare_pave_trace_diff_metabolite(): Export PAVE vs TRACE metabolite assignment table
export_instrument_parameters(): Export PAVE2 instrument-parameter table to Excel
extract_cn_labeling_forms(): Match m/z / RT and extract all CN labeling forms for a metabolite
extract_instrument_params(): Extract acquisition parameters from a Thermo `.raw` file
find_c12n14_raw(): Find C12N14 replicate-001 raw file in a PAVE2 dataset folder
get_TRACE_CN_labelling_ratio(): Get CN labelling ratio for TRACE seeds
list_pave2_datasets(): List PAVE2 instrument folders containing C12N14 raw files
map_pave_seed_vertex_group(): Map PAVE pave_seed (m/z) to vertex group labels for network plots
nutrition_merge_top_absorb_forms(): Merge top absorb forms selected per group
nutrition_met_label(): Build a display label for a nutrient-analysis metabolite
nutrition_select_top_absorb_forms(): Select top absorb forms per nutrient group
nutrition_summarize_absorb_global(): Summarize absorb forms with atom-count-weighted scores
plot_TRACE_RSD(): Plot feature RSD distribution by sample group
plot_TRACE_labeling_fraction(): Plot TRACE CN labeling fraction per metabolite and sample
plot_TRACE_labeling_fraction_nutrients(): Plot TRACE CN labeling fraction for nutrient sample groups
plot_TRACE_network_split_demo(): Plot a TRACE network split demo colored by assignment group
plot_compare_pave_adduct(): Plot PAVE vs TRACE adduct selection comparison
plot_compare_pave_adduct_conflict_demo(): Plot one ranked adduct-conflict seed-chain demo
plot_compare_pave_annotation_change_summary(): Annotation-type cross-tab summary (TRACE vs PAVE)
plot_compare_pave_cn_bundle(): Plot CN bundle correlation and m/z error for PAVE vs TRACE groups
plot_compare_pave_dyn_filtered_xic(): Plot XIC comparison for dynamic-filtered vs overlap CN seeds
plot_compare_pave_fragment(): Plot PAVE fragment vs TRACE annotation comparison
plot_compare_pave_lib_assignment_error(): Boxplot + points: dynamic-filter vs overlap CN-bundle errors
plot_compare_pave_lib_assignment_error_scatter(): Scatter: CN-bundle m/z vs RT error with dynamic-filter cutoffs
plot_compare_pave_wrong_cn_feature_demo(): Plot one wrong-CN demo for a specific feature
plot_compare_pave_wrong_cn_pave_demo(): Plot one wrong-CN-in-PAVE CN-bundle demo
plot_ratio_shift_by_intensity(): Plot ratio-shift distributions by seed intensity
plot_ratio_shift_by_ion_form(): Plot ratio-shift distributions by TRACE adduct form
plot_ratio_shift_by_platform(): Plot ratio-shift distributions by instrument platform
plot_ratio_shift_distribution(): Plot ratio-shift distributions across platforms, ion forms, and intensity
plot_xcms_xic_cn_groups(): ggplot2 four-group XIC (chrom + per-group m/z strips)
read_thermo_raw_meta_dump(): Run ThermoRawMetaDump on a Thermo `.raw` file
run_absorb_form_analysis(): Run absorb-form analysis for one polarity
summarize_ratio_shift(): Summarize ratio-shift by platform or TRACE adduct form