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 |
aid |
An assay ID |
cid |
A list of CID's |
sid |
A list of SID's |
quiet |
If |
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
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