Description Usage Arguments Details Value Examples
This function can be used to query compound annotations from the default
resources as well as the custom resources stored in the SQLite annotation
database. The default annotation resources are DrugAge, DrugBank, CMAP02 and
LINCS. Detailed description of the SQLite database is available at the
corresponding compoundCollectionData
package. The customized compound annotations could be added/deleted by the
customAnnot
utilities.
1 | queryAnnotDB(chembl_id, annot = c("DrugAge", "DrugBank", "CMAP02", "LINCS"))
|
chembl_id |
character vector of ChEMBL IDs. |
annot |
character vector of annotation resources, such as
|
The input of this query function is a set of ChEMBL IDs, it returns a
data.frame storing annotations of the input compounds from selected
annotation resources defined by the annot
argument.
data.frame of annotation result
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | query_id <- c("CHEMBL1000309", "CHEMBL100014", "CHEMBL100109",
"CHEMBL100", "CHEMBL1000", "CHEMBL10")
annot_res <- queryAnnotDB(query_id, annot=c("DrugAge", "LINCS"))
# Add a custom compound annotation table
chembl_id <- c("CHEMBL1000309", "CHEMBL100014", "CHEMBL10",
"CHEMBL100", "CHEMBL1000", NA)
annot_tb <- data.frame(compound_name=paste0("name", 1:6),
chembl_id=chembl_id,
feature1=paste0("f", 1:6),
feature2=rnorm(6))
addCustomAnnot(annot_tb, annot_name="mycustom")
# query custom annotation
annot_res2 <- queryAnnotDB(query_id, annot=c("LINCS", "mycustom"))
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