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 (mass-spectrometry metabolomics object)
AddSiriusAnnot(): Adding annotation from SIRIUS to the mmo
AddChemSim(): Add chemical similarity matrices to the mmo
AddCustomSim(): Add a custom feature similarity matrix to the mmo
AddChemDist(): Add chemical distance matrices to the mmo
AddCustomDist(): Add a custom feature distance matrix to the mmo
AddCustomAnnot(): Add custom annotations to a mmo
ReplaceZero(): #' Replace zero and NA values in the mmo
MassNormalization(): Use sample mass in the metadata file to normalize the peak area
LogNormalization(): Log-normalize the peak area in the mmo
MeancenterNormalization(): Mean-center the peak area in the mmo
ZNormalization(): Z-normalize the peak area in the mmo
ReorderGroups(): Reorder samples in the mmo based on group order
SwitchGroup(): Switch the group column in the mmo
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 a mmo 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 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
GetDAMs(): Generates lists of DAMs (Differentially Accumulated Metabolites) for each comparison in the mmo
GetLog2FoldChange(): Calculate log2 fold change for a given control group
GetGroupMeans(): Calculate group means from the mmo
VolcanoPlot(): Volcano plot for visualizing differential metabolite analysis results
AnovaBarPlot(): Generate barplots for each feature and perform ANOVA
GenerateHeatmapInputs(): GenerateHeatmapInputs (similarity-based)

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 (similarity-based)
GetBetaDiversity(): GetBetaDiversity (similarity-based)
GetRichness(): GetRichness
GetHillNumbers(): GetHillNumbers
GetFunctionalHillNumber(): GetFunctionalHillNumber (similarity-based)
GetFaithPD(): GetFaithPD (similarity-based)
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 (similarity-based)
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 a mmo previously saved with SaveMMO
ExportFeaturesToCSV(): ExportFeaturesToCSV
pool_mmo_by_group(): pool_mmo_by_group

Utilities

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

GetSimMat(): Retrieve a feature similarity matrix from the mmo
GetDistanceMat(): Get the distance matrix from the mmo based on the specified distance metric
GetNormFeature(): Retrieve feature data from the mmo, with normalization options
FeatureToID(): Convert feature names to IDs in the mmo
IDToFeature(): Convert feature IDs to names in the mmo
print(<mmo>): Print method for mmos 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
write_anova(): Write results of anova_tukey_dunnett to a CSV file
permanova_stat(): Perform PERMANOVA and pairwise comparisons

Dissimilarity-based versions (superseded)

Retained versions of the diversity and dendrogram functions that read the older .dissim slots written by AddChemDist(). The functions without the _derep suffix read the .sim slots written by AddChemSim() and are the recommended entry points.

GetAlphaDiversity_derep(): GetAlphaDiversity
GetBetaDiversity_derep(): GetBetaDiversity
GetFaithPD_derep(): GetFaithPD
GetFunctionalHillNumber_derep(): GetFunctionalHillNumber
FeatureDendrogram_derep(): FeatureDendrogram
GenerateHeatmapInputs_derep(): Generate input files to be used for pheatmap from the mmo