create an OmicSignature object from differential expression matrix

updated 08/2025

Usage

OmicSigFromDifexp(difexp, metadata, criteria = NULL)

difexp: Differential expression matrix
metadata: Metadata for the OmicSignature object. If `criteria` is `NULL`, the criterias to extract signatures will need to be provided in metadata. They can be specified in metadata fields as one or more of the followings: `logfc_cutoff`, `score_cutoff`, `adj_p_cutoff`, `p_value_cutoff`.
criteria: A character string of R expressions used to extract signatures from difexp, e.g. "logfc > 5; score > 10", evaluated as R code (via `rlang::parse_exprs()`) against `difexp` - `criteria` must only ever come from a trusted source, not from untrusted/external input. Alternatively, they can be provided in metadata fields: list("logfc_cutoff" = 5, "score_cutoff" = 10). At least one of `criteria` or a metadata cutoff field is required; without any, every row of `difexp` would silently become the signature.

OmicSignature object