Example S2IsoMEr ORA Object
example_ORA_obj.RdThe example_ORA_obj dataset is a pre-built S2IsoMEr enrichment object. This object was created using the initEnrichment() function and contains all the necessary parameters for performing bootstrapping-based ORA.
Usage
data(example_ORA_obj)Format
An object of class S2IsoMEr with the following components:
- scmatrix
A numeric matrix of metabolite measurements, with rows representing metabolites and columns representing cells or measurements.
- polarization_mode
Character indicating the polarization mode, either "positive" or "negative".
- enrichment_type
Character specifying the enrichment analysis type, either "ORA" or "MSEA".
- Annotation_database
Character or character vector specifying the annotation database(s) used, e.g., "CoreMetabolome", "HMDB", "SwissLipids", or "LipidMaps".
- Custom_database
Optional custom annotation database provided as a dataframe with two columns: "formula" and "molecule name".
- annotations
A list of length
n, where each element contains a vector of isomer names associated with each metabolite.- annotation.weights
An optional list of length
n, with each element containing a vector of isomer weights.- isobars_list
A list of isobaric species, only used when
consider_isobars = TRUE.- conditions
A vector of condition identifiers, with length equal to the number of columns in
scmatrix.- include
A logical vector indicating which metabolites to include in the analysis.
- consider_isomers
Logical indicating whether isomers are considered in the analysis.
- consider_isobars
Logical indicating whether isobars are included in the analysis.
- mass_range_ppm
Numeric indicating the mass range (in ppm) for isobar identification.
- background_name
Character specifying the enrichment background type, either "custom" or a combination of molecule and background types.
- endogenous_only
Logical indicating whether to only consider endogenous metabolites.
- pathway_assoc_only
Logical indicating whether to include only metabolites associated with a biological pathway.
- remove_expected_predicted
Logical indicating whether to remove expected or predicted isomers based on HMDB status.
- pathway_list
A list of pathways associated with the analyzed metabolites.
- LUT
A lookup table used for annotating metabolites.
- termsSelection
Character specifying the terms of interest for the enrichment analysis.
- condition.x
Character specifying the first condition identifier for pairwise comparison.
- condition.y
Character specifying the second condition identifier for pairwise comparison.
- ranking.by
Character specifying the ranking method used in MSEA, e.g., "wilcox.test", "t.test", "logFC", or "BWS".
- gsea.method
Character specifying the GSEA method, either "ks_signed" or "fgsea".
Examples
# Load the example dataset
data(example_ORA_obj)