Skip to contents

Run hypeR.GEM enrichment directly from SigRepo metabolomics signatures

runHyperGEM.Rd

Resolves one or more metabolomics signatures from SigRepo and runs hypeR.GEM without requiring the user to call getSignature() manually first.

Usage

runHyperGEM(
  conn_handler = NULL,
  signature_id = NULL,
  signature_name = NULL,
  omic_signature = NULL,
  genesets,
  reference_key = NULL,
  species = "human",
  directional = TRUE,
  merge = TRUE,
  promiscuous_threshold = 10,
  ensemble_id = FALSE,
  background = NULL,
  method = c("weighted", "unweighted"),
  weighted_by = "one_minus_fdr",
  min_metabolite = 1,
  score_col = "score",
  split_by_group = TRUE,
  split_by_direction = TRUE,
  verbose = TRUE
)

Arguments

conn_handler

An R object obtained from SigRepo::newConnHandler(). Required unless omic_signature is supplied.

signature_id

One or more SigRepo signature IDs.

signature_name

One or more SigRepo signature names.

omic_signature

A single OmicSignature object or a list of OmicSignature objects.

genesets

A named list of genesets, a hypeR gsets object, or a hypeR rgsets object.

reference_key

Optional metabolite identifier column to use for GEM mapping.

species

Species passed to hypeR.GEM::signature2gene(). Defaults to "human".

directional

Logical; whether to use directional mapping in hypeR.GEM::signature2gene().

merge

Logical; whether to merge mapped metabolites in hypeR.GEM::signature2gene().

promiscuous_threshold

Numeric threshold passed to hypeR.GEM::signature2gene().

ensemble_id

Logical; passed to hypeR.GEM::signature2gene().

background

Optional background passed to hypeR.GEM.

method

One of "weighted" or "unweighted".

weighted_by

Weighting field passed to hypeR.GEM::enrichment() for weighted GEM analyses.

min_metabolite

Minimum metabolite count passed to GEM enrichment.

score_col

Column containing directional scores in the metabolomics signature table.

split_by_group

Logical; whether to split GEM signatures by group_label.

split_by_direction

Logical; whether to split GEM signatures into up and down subsets when a numeric score column is available.

verbose

Logical; whether or not to print diagnostic messages while retrieving signatures.

Value

A list with result, signatures, metadata, gem_object, and reference_key.

Examples

if (FALSE) { # \dontrun{
gem_res <- SigRepo::runHyperGEM(
  conn_handler = conn_handler,
  signature_name = "example_metabolomics_signature",
  genesets = genesets,
  method = "weighted"
)
} # }