run.sea: run SEA

In momeara/SEAR: R Tools for working with the Similarity Ensemble Approach Program

Description

inputs: background_fname: filename of .fit file ref_set: compound sets for reference targets path to .set file or data.frame with columns [target, name, compound] ref_smi: compounds for reference targets path to .smi file or data.frame with columns [compound, smiles] query_set: compound sets for query targets path to .set file or data.frame with columns [target, name, compound] query_smi: compounds for query targets path to .smi file or data.frame with columns [compound, smiles] run_tag: a tag given help identify the sea analysis in the SEA viewer default NULL output_base: path and file prefix where the files should be written default to a temporary file

Usage

run.sea(background_fname, ref_set, ref_smi, query_set, query_smi,
  run_tag = NULL, output_base = NULL, similarity_measure = "tanimoto",
  tversky_alpha = 0.5, tversky_beta = 0.5)

Details

Output: data.frame with columns [target1, target2, EValue, MaxTC] for SEA associations export

momeara/SEAR documentation built on May 23, 2019, 6:09 a.m.