Retrieve STRING interactions for selected assay features — network_string • bulkMAE

Retrieve STRING interactions for selected assay features

Usage

network_string(
  x,
  experiment,
  assay,
  genes = NULL,
  species = 9606,
  version = "12.0",
  score_threshold = 400,
  input_directory = "",
  remove_unmapped = TRUE
)

Arguments

x: A MultiAssayExperiment object.
experiment: Optional experiment name.
assay: Assay name or one-based assay index.
genes: Optional feature identifiers; defaults to assay row names.
species: NCBI taxonomy identifier.
version: STRING database version.
score_threshold: Minimum STRING score.
input_directory: Optional STRING download/cache directory.
remove_unmapped: Remove identifiers not mapped by STRING.

Value

A data frame of STRING interactions.