computeSimilarity: Compute Tanimoto similarity network
In kwanjeeraw/metabox: metabox

Description Usage Arguments Value Note Author(s) References See Also Examples

compute a network for compounds based on chemical structure similarity. The function computes Tanimoto distances between the given compounds using PubChem fingerprints.

1	computeSimilarity(txtinput, coef, returnas)

`txtinput`	a character vector of PubChem CIDs.
`coef`	a numeric value specifying the minimum Tanimoto similarity correlation coefficient to be included in the output (from 0 to 1, default is 0.7).
`returnas`	a string specifying output type. It can be one of dataframe, list, json. Default is dataframe.

list of network information with the following components:

nodes:

id = pubchem CID or node neo4j id

gid = pubchem CID

nodename = pubchem CID or node name

nodelabel = node type

edges:

source, target = pubchem CID or node neo4j id

coef = Tanimoto similarity coefficient

type = relationship type

Return empty list if error or found nothing.

If the database is installed, node attributes will be automatically retrieved from the database. Otherwise node attributes will be the original input.

Kwanjeera W kwanich@ucdavis.edu

Willett P., Barnard JM. and Downs GM. (1998) Chemical similarity searching. J. Chem. Inf. Comput. Sci., 38, 983–996.

Barupal KD., et al. (2012) MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. BMC Bioinformatics. 13:99.

Grapov D., Wanichthanarak K. and Fiehn O. (2015) MetaMapR: pathway independent metabolomic network analysis incorporating unknowns. Bioinformatics. 31(16):2757-60.

Cao Y., Charisi A., Cheng L., Jiang T. and Girke T. (2008) ChemmineR: a compound mining framework for R. Bioinformatics, 24(15), pp. 1733–1734.

ftp://ftp.ncbi.nih.gov/pubchem/specifications/pubchem_fingerprints.txt

metabomapr, CID_tanimoto, fpSim, sdfid