with_dbi: Load a SQL database file and run a function from the...

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Load a SQL database file and run a function from the AnnotationDbi package.

Description

An AnnotationDbi object cannot be used in parallel, so this is a workaround.

Usage

with_dbi(annotation_db_file, dbi_fun, ...)

Arguments

annotation_db_file	A character scalar: path to SQLite file of annotation DB, e.g. org.Hs.eg.db$conn@dbname.
dbi_fun	A function from the AnnotationDbi package which accepts AnnotationDbi object as parameter x, e.g. AnnotationDbi::mapIds().
...	Parameters passed to dbi_fun.

Value

An output from dbi_fun.

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.