get.assay {rpubchem}R Documentation

Get a PubChem Bio-Assay

Description

PubChem provides access to a number of bio-assays which are generally results obtained from High Throughput Screens (HTS). The number of observations in a given assay can be as high as 42000. This method allows one to obtain the assay data for a given assay ID. Assay ID's can be obtained using a text search using the find.assay.id function.

Usage

get.assay(aid, quiet=TRUE)

Arguments

aid An assay ID
quiet If FALSE the output is verbose

Details

The assay data are obtained for a variety of targets using a variety of techniques. As a result though each assay dataset contains a set of fixed fields, they can have additional fields.

Value

A data frame with the observations in the rows. The number of columns varies from assay to assay. Any assay will, however, have the following columns:

PUBCHEM.SID PubChem SID
PUBCHEM.CID PubChem CID
PUBCHEM.ACTIVITY.OUTCOME Activity outcome
PUBCHEM.ACTIVITY.SCORE Activity score, higher is more active
PUBCHEM.ASSAYDATA.COMMENT Test result specific comment
description A short description of the assay
comments Comments associated with the assay
types A named list where the names are the assay specific field names. Each element of the list is a 2-element vector containing the description of the field along with the units. In case the field is unitless the unit is NA

normal-bracket34bracket-normal

Author(s)

Rajarshi Guha rguha@indiana.edu

See Also

get.assay.desc, find.assay.id


[Package rpubchem version 1.4.2 Index]