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
1 | #simnw <- computeSimilarity(c(1110,10413,196,51,311,43,764,790)) #compute similarity network for given pubchem compounds
|
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