Package index • S2IsoMEr

All functions

Load_background(): Load enrichment background

Run_bootstrap_MSEA(): Run Bootstrapped Metabolite Set Enrichment Analysis (MSEA)

Run_bootstrap_ORA(): Wrapper function for Bootstrap Over-Representation Analysis (ORA)

Run_enrichment(): Run Metabolite/Lipids enrichment analysis for single cell metabolomics

Run_simple_MSEA(): Run Simple Metabolite Set Enrichment Analysis (MSEA)

Run_simple_ORA(): Wrapper function for Simple Over-Representation Analysis (ORA)

barplot_MSEA_boot(): Plot bootstrap enrichment analysis

barplot_ORA_boot(): Bar Plot for ORA Bootstrapped Results

barplot_ORA_simple(): Bar Plot for Simple ORA Results

build_iso_bg(): Build Isomer/Isobar Background

calc_LFC_scmat(): Calculate Log Fold Change (LFC) from Single-Cell Metabolomics Matrix

compare_metabo_distr(): Plot intensity distribution of metabolite across conditions

decouple_ORA_wrapper(): Run ORA Analysis with Optional Bootstrapping

dotplot_ORA(): Dot Plot for Over-Representation Analysis (ORA) Results

example_MSEA_multicond: Example Multi condition MSEA results

example_MSEA_obj: Example S2IsoMEr MSEA Object

example_ORA_custom_universe: Example custom universe for ORA

example_ORA_markers: Example List of Markers for ORA

example_ORA_obj: Example S2IsoMEr ORA Object

get_TP_markers_per_Term(): Get intersection between term and query for a Specific Term

get_metabo_iso(): Get Metabolite Isomers and Isobars

initEnrichment(): Generate S2IsoMEr enrichment object

map_TP_markers_to_ions(): Map True Positive Markers to Input Ions from single cell matrix.

metabo_bootstrap(): Perform Bootstrap Sampling on Metabolite Annotations

passed_filters_per_term(): Report filters applied to bootstrap-based enrichment results

plot_MSEA_Multi_cond(): Plot Heatmap of MSEA Results Across Multiple Conditions

rankScore(): Rank metabolites for S2IsoMEr enrichment object

ridge_bootstraps(): Ridge Plot of Bootstrap Enrichment Results for Terms of Interest

setConditions(): Set conditions for enrichment analysis

simple_fgsea(): Run simple fGSEA enrichment