getassay: Get a PubChem Bio-Assay
In CDK-R/rpubchem: An Interface to the PubChem Collection

Description Usage Arguments Details Value Author(s) See Also

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.

1	get.assay(aid, cid=NULL, sid=NULL, quiet=TRUE)

`aid`	An assay ID
`cid`	A list of CID's
`sid`	A list of SID's
`quiet`	If `FALSE` the output is verbose

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.

If cid or sid is not specified the entire bioassay is retrieved. This can be time consuming for primary screening assays. If both arguments are specified, then sid is used in preference to sid.

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

The activity outcome field is provided as a numeric but is recoded as described in the PubChem documentation. The remaining fields are obtained by parsing the description file for the corresponding assay.

In addition to the usual attributes for a data.frame object this function adds some extra attributes:

descriptionA short description of the assay
commentsComments associated with the assay
typesA 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

Rajarshi Guha rajarshi.guha@gmail.com

get.assay.desc, find.assay.id

CDK-R/rpubchem documentation built on Nov. 6, 2019, 3:59 a.m.