getaidcid: Get Assay ID Based on Compound Activity
In rpubchem: rpubchem - Interface to the PubChem Collection

Description Usage Arguments Details Value Author(s) See Also

This function allows you to identify PubChem assays in which a compound, specified by CID, has been tested in. The method uses the PubChem Power User Gateway (PUG) and as a result can be slow.

The function can be used to identify assays in which the CID is active, inactive, discrepant in, or simply the assays in which it has been tested.

However, since the query can be slow, it is useful have the raw data. In such a case, one can get an indicator matrix which can be processed to identify assays in which the compound are active, inactive, etc.

1	get.aid.by.cid(cid, type="raw", quiet=TRUE)

`cid`	A single compound ID
`type`	What type of query should be performed. Valid values are 'active', 'inactive', 'discrepant', 'tested' or 'raw'.
`quiet`	If `FALSE`, output is verbose

Since the method employs PUG, it is rather slow. In addition it can also fail intermittently. In general, as long as the CID is correctly specified, a pause between subsequent calls usually allows the query to successfully complete

If the type argument was one of 'active', 'inactive', 'discrepant' or 'tested' a numeric vector of assay IDs. If 'raw' was specifiec, a binary matrix is returned with the number of rows equal to the number of assays the compound was tested in and 4 columns - aid, active, inactive, discrepant. If a row has a a 1 in columns 2 to 4, it indicates that the compound is either active, inactive or discrepant.

In case an invalid CID was specified or the query failed, NULL is returned.

Rajarshi Guha rguha@indiana.edu

get.assay

rpubchem documentation built on May 2, 2019, 5:53 p.m.