Package index • ecomet

Core dataset processing

Build and populate the mmo object from MZmine outputs and annotation tools.

GetMZmineFeature(): Import MZmine feature table and metadata to create a mmo object

AddSiriusAnnot(): Adding annotation from SIRIUS to the mmo object

AddChemDist(): Add chemical distance matrices to the mmo object

AddCustomDist(): Add a custom feature distance matrix to the mmo object

AddCustomAnnot(): Add custom annotations to an mmo object

ReplaceZero(): #' Replace zero and NA values in the mmo object

MassNormalization(): Use sample mass in the metadata file to normalize the peak area

LogNormalization(): Log-normalize the peak area in the mmo object

MeancenterNormalization(): Mean-center the peak area in the mmo object

ZNormalization(): Z-normalize the peak area in the mmo object

ReorderGroups(): Reorder samples in the mmo object based on group order

SwitchGroup(): Switch the group column in the mmo object

FeaturePresence(): Convert feature abundances to presence / absence

Filtering

Subset the mmo object by samples, groups, or features, and keep associated MGF spectral files in sync.

filter_mmo(): Filter an mmo object by samples, groups, and/or features

filter_mgf_to_mmo(): Filter an MGF file to keep only spectra for features present in mmo$feature_data$id

annotate_feature_info_ms2_from_mgf(): Annotate mmo$feature_info with MS2 presence and MS2 block counts from an MGF

filter_canopus_annotations(): Filter CANOPUS / SIRIUS annotations in an ecomet mmo object by probability threshold

filter_cosmic_structure(): Filter SIRIUS structure (CSI:FingerID) annotations by COSMIC confidence score

Differential analysis & visualization

Identify and visualize differentially accumulated metabolites between groups.

PairwiseComp(): Perform pairwise comparison between two groups in the mmo object

GetDAMs(): Generates lists of DAMs (Differentially Accumulated Metabolites) for each comparison in the mmo object

GetLog2FoldChange(): Calculate log2 fold change for a given control group

GetGroupMeans(): Calculate group means from the mmo object

VolcanoPlot(): Volcano plot for visualizing differential metabolite analysis results

AnovaBarPlot(): Generate barplots for each feature and perform ANOVA

GenerateHeatmapInputs(): Generate input files to be used for pheatmap from the mmo object

Ordination & clustering

Multivariate methods for comparing samples and groups.

PCAplot(): Plots PCA and performs PERMANOVA

PLSDAplot(): PLS-DA plot with feature loadings

NMDSplot(): NMDSplot

PCoAplot(): PCoAplot

HCplot(): HCplot

Chemical diversity

Alpha and beta diversity metrics incorporating feature abundance and chemical distances.

GetAlphaDiversity(): GetAlphaDiversity

GetBetaDiversity(): GetBetaDiversity

GetRichness(): GetRichness

GetHillNumbers(): GetHillNumbers

GetFunctionalHillNumber(): GetFunctionalHillNumber

GetFaithPD(): GetFaithPD

RarefactionAUC(): RarefactionAUC

CalculateGroupBetaDistance(): CalculateGroupBetaDistance

GetSpecializationIndex(): GetSpecializationIndex

Chemical class analysis

Enrichment and visualization of compound classes using SIRIUS/CANOPUS annotations.

CanopusLevelEnrichmentAnal(): Enrichment analysis for Canopus-predicted terms

CanopusListEnrichmentPlot(): Generate a plot for enrichment analysis of Canopus-predicted terms

CanopusListEnrichmentPlot_2(): Generate a plot for enrichment analysis of Canopus-predicted terms across multiple levels

CanopusLevelEnrichmentPlot(): Generate a plot for enrichment analysis of Canopus-predicted terms at a specific level using a list of vectors of features

CanopusAllLevelEnrichmentPlot(): Generate a plot for enrichment analysis of Canopus-predicted terms across all levels

PlotNPCStackedBar(): PlotNPCStackedBar

MSEA(): Metabolite Set Enrichment Analysis (MSEA)

Compound networks & dendrograms

Build chemical similarity trees and export to iTOL or Cytoscape.

FeatureDendrogram(): FeatureDendrogram

PlotFeatureDendrogram(): PlotFeatureDendrogram

ExportITOL(): ExportITOL

ExportCytoscape(): ExportCytoscape

Phenotype association

Correlate individual features or metabolite sets with continuous ecological variables.

FeaturePhenotypeCorrelation(): FeaturePhenotypeCorrelation

ScreenFeaturePhenotypeCorrelation(): Screen feature-phenotype correlation

GetPerformanceFeatureCorrelation(): GetPerformanceFeatureCorrelation

GetPerformanceFeatureLMM(): GetPerformanceFeatureLMM

GetPerformanceFeatureRegression(): GetPerformanceFeatureRegression

PlotFoldchangeResistanceQuad(): PlotFoldchangeResistanceQuad

PlotFoldchangeResistanceRegression(): PlotFoldchangeResistanceRegression

PlotFoldchangeResistanceRegression_t(): PlotFoldchangeResistanceRegression_t

Save & export

Save mmo objects and export results.

SaveMMO(): Save entire mmo object to a file (RDS)

LoadMMO(): Load an mmo object previously saved with SaveMMO

ExportFeaturesToCSV(): ExportFeaturesToCSV

pool_mmo_by_group(): pool_mmo_by_group

Utilities

Helper functions for data access, formatting, and internal calculations.

GetDistanceMat(): Get the distance matrix from the mmo object based on the specified distance metric

GetNormFeature(): Retrieve feature data from the mmo object, with normalization options

FeatureToID(): Convert feature names to IDs in the mmo object

IDToFeature(): Convert feature IDs to names in the mmo object

print(<mmo>): Print method for mmo objects Provides a clean, human-readable overview of an mmo list object instead of dumping the entire list when the object is printed in the console.

anova_tukey_dunnett(): Perform ANOVA and Tukey's HSD test on the mmo object

write_anova(): Write results of anova_tukey_dunnett to a CSV file

permanova_stat(): Perform PERMANOVA and pairwise comparisons