Run hypeR enrichment directly from SigRepo signatures

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

Usage

runHypeR(
  conn_handler = NULL,
  signature_id = NULL,
  signature_name = NULL,
  omic_signature = NULL,
  genesets = NULL,
  msigdb_species = "Homo sapiens",
  msigdb_collection = NULL,
  msigdb_subcollection = NULL,
  msigdb_clean = FALSE,
  method = c("hypergeo", "kstest", "gsea"),
  feature_col = "feature_name",
  score_col = "score",
  split_by_group = FALSE,
  split_by_direction = FALSE,
  background = NULL,
  fdr = 0.05,
  plotting = FALSE,
  quiet = TRUE,
  absolute = FALSE,
  power = 1,
  ...,
  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 supplied to hypeR. Alternatively, leave this as NULL and specify msigdb_collection to fetch genesets from MSigDB automatically.
msigdb_species: Species passed to hypeR::msigdb_gsets() when msigdb_collection is supplied. Defaults to "Homo sapiens".
msigdb_collection: MSigDB collection identifier, such as "H" or "C2". When supplied, runHypeR() retrieves genesets automatically via hypeR::msigdb_gsets().
msigdb_subcollection: Optional MSigDB subcollection identifier, such as "CP:KEGG_LEGACY".
msigdb_clean: Logical; whether to clean MSigDB geneset labels using hypeR::msigdb_gsets(clean = ...). Defaults to FALSE.
method: One of "hypergeo", "kstest", or "gsea".
feature_col: Column containing feature identifiers. Defaults to "feature_name".
score_col: Column containing ranked scores for KS/GSEA-style enrichment. Defaults to "score".
split_by_group: Logical; whether to create separate query vectors for each group_label. Defaults to FALSE.
split_by_direction: Logical; when method = "hypergeo", whether to split each group into up- and down-direction feature sets using the sign of score_col. Defaults to FALSE.
background: Optional background size passed to hypeR.
fdr: FDR threshold passed to hypeR. Defaults to 0.05.
plotting: Logical; whether to let hypeR generate plots. Defaults to FALSE.
quiet: Logical; whether to suppress hypeR messages. Defaults to TRUE.
absolute: Passed to hypeR for GSEA-style ranked enrichment. Defaults to FALSE.
power: Passed to hypeR for GSEA-style ranked enrichment. Defaults to 1.
...: Additional arguments passed directly to hypeR::hypeR(). Use this for extra tuning parameters such as background or other engine-specific options.
verbose: Logical; whether or not to print diagnostic messages while retrieving signatures. Defaults to TRUE.

Value

A list with:

result: A hyp or multihyp object returned by hypeR.
signatures: The query vectors passed into hypeR.
metadata: A data frame describing each query vector.

Examples

if (FALSE) { # \dontrun{
hyp_res <- SigRepo::runHypeR(
  conn_handler = conn_handler,
  signature_name = "example_signature",
  msigdb_collection = "H",
  method = "hypergeo",
  background = 20000
)
} # }