get.assay:
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, cid=NULL, sid=NULL, quiet=TRUE)
Arguments
quiet
If FALSE the output is verbose
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: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
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. 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.