Package index • ecomet

Core dataset processing

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

AddCustomAnnot(): Add custom annotations to an mmo object

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

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

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

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

ReplaceZero(): #' Replace zero and NA values 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

Filterng MMO and associated MGF

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

Basic statistics and visualization

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

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

PCAplot(): Plots PCA and performs PERMANOVA

PLSDAplot(): PLS-DA plot with feature loadings

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

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

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

GetGroupMeans(): Calculate group means from the mmo object

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

HCplot(): HCplot

Chemical class analysis

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

MSEA(): Metabolite Set Enrichment Analysis (MSEA)

Chemical diversity Analysis

GetAlphaDiversity(): GetAlphaDiversity

GetBetaDiversity(): GetBetaDiversity

NMDSplot(): NMDSplot

PCoAplot(): PCoAplot

CalculateGroupBetaDistance(): CalculateGroupBetaDistance

GetSpecializationIndex(): GetSpecializationIndex

PlotNPCStackedBar(): PlotNPCStackedBar

RarefactionAUC(): RarefactionAUC

Metadata regression analysis

FeaturePhenotypeCorrelation(): FeaturePhenotypeCorrelation

ScreenFeaturePhenotypeCorrelation(): Screen feature-phenotype correlation

GetPerformanceFeatureCorrelation(): GetPerformanceFeatureCorrelation

GetPerformanceFeatureLMM(): GetPerformanceFeatureLMM

GetPerformanceFeatureRegression(): GetPerformanceFeatureRegression

PlotFoldchangeResistanceQuad(): PlotFoldchangeResistanceQuad

PlotFoldchangeResistanceRegression(): PlotFoldchangeResistanceRegression

PlotFoldchangeResistanceRegression_t(): PlotFoldchangeResistanceRegression_t

Output

ExportFeaturesToCSV(): ExportFeaturesToCSV

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

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

misc

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

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

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

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

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

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

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.

GetFaithPD(): GetFaithPD

GetFunctionalHillNumber(): GetFunctionalHillNumber

GetHillNumbers(): GetHillNumbers

GetRichness(): GetRichness

pool_mmo_by_group(): pool_mmo_by_group