Calculates Significant Metabolic Pathways using a Fisher Exact Test

Usage

FishersPathwayAnalysis(
  Analyte,
  max_path_size = 500,
  min_path_size = 5,
  alternative = "greater",
  pathway_all_info = FALSE,
  pval_cutoff = NULL,
  verbose = TRUE,
  ...
)

Arguments

Analyte

A list of analytes containing a combination of three possible elements, namely "mzs", "genes" and/or "metabolites". The list must be named with these titles, corresponding to the relative input datasets. Read below for supported input formats.

max_path_size

The max number of in a specific pathway (default = 500).

min_path_size

The min number of in a specific pathway (default = 5).

alternative

The hypothesis of the fisher exact test (default = "greater").

pathway_all_info

Whether to included all genes/ screened in the return (default = FALSE).

pval_cutoff

A numerical value defining the adjusted p value cutoff for keeing significant pathways (default = NULL).

verbose

Boolean indicating whether to show informative messages. If FALSE these messages will be suppressed (default = TRUE).

...

Additional parameters that can be passed through to annotateTable() when running mz-based analysis. Please see documentation for annotateTable() for more details.

Details

Supported metabolites format: strings which contain the metabolite ID with database name. For example = "hmdb:HMDBX", "chebi:X", "pubchem:X","wikidata:X" ,"kegg:X" ,"CAS:X","lipidbank:X","chemspider:X"," LIPIDMAPS:X" (where X stands for upper case of the cooresponding ID in each database)
Supported genes data format: strings which contain the gene name and formatting. For example = "entrez:X", "gene_symbol:X", "uniprot:X", "ensembl:X", "hmdb:HMDBPX"
Supported mzs format: any string or numeric vector contains the m/z. NOTE: If mzs values are provided then annotateTable() will be run using default parameters and combining the Chebi_db, Lipidmaps_db and HMDB_db databases.

Value

a dataframe with the relevant pathway information

Examples

## Running in 'mzs' mode:
# FishersPathwayAnalysis(Analyte = list("mzs" = mz_values), ppm_error = 3)

## Running in 'metabolites' mode
# FishersPathwayAnalysis(Analyte = list("metabolites" = metabolite_ids))

## Running 'metabolites' and 'genes' combined
# FishersPathwayAnalysis(Analyte = list("metabolites" = metabolite_ids, "genes" = gene_names))