customAnnot: Add/Delete Custom Annotation

In yduan004/customCMPdb: Customize and Query Compound Annotation Database

Description

Functions could be used to add/delete user's custom compound annotations from the annotation SQLite database. The added custom compound annotation table should contains a column named as chembl_id that represents the ChEMBL ids of the added compounds.

The listAnnot function lists the available annotation resources in the SQLite annotation database.

The defaultAnnot function sets the annotation SQLite database to the default one by deleting the existing one and re-downloading from AnnotationHub.

Usage

addCustomAnnot(annot_tb, id_col = NULL, annot_name, overwrite = FALSE)

deleteAnnot(annot_name)

listAnnot()

defaultAnnot()

Arguments

annot_tb	data.frame representing the custom annotation table, Note, it should contains a 'chembl_id' column representing the compound ChEMBL ids
id_col	column name in annot_tb that is used as ID column, this column must contain unique identifiers. If not defined, an automatically generated ID column will be appended.
annot_name	character(1), user defined name of the annotation table
overwrite	a logical specifying whether to overwrite an existing table or not. Its default is FALSE.

Value

character vector of names of the annotation tables in the SQLite DB

character(1), path to the annotation SQLite database

Examples

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="mycustom3")
deleteAnnot("mycustom3")
annot_names <- listAnnot()
# defaultAnnot()

yduan004/customCMPdb documentation built on Feb. 3, 2022, 2:10 p.m.