Get Assay ID Based on Compound Activity

Description

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.

Usage

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

Arguments

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

Details

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

Value

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.

Author(s)

Rajarshi Guha rguha@indiana.edu

See Also

get.assay