ensembldb: convertFilter – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

convertFilter

Convert an AnnotationFilter to a SQL WHERE condition for EnsDb

Description

convertFilter converts an AnnotationFilter::AnnotationFilter or AnnotationFilter::AnnotationFilterList to an SQL where condition for an EnsDb database.

Usage

## S4 method for signature 'AnnotationFilter,EnsDb'
convertFilter(object, db, with.tables = character())

## S4 method for signature 'AnnotationFilterList,EnsDb'
convertFilter(object, db, with.tables = character())

Arguments

`object`	`AnnotationFilter` or `AnnotationFilterList` objects (or objects extending these classes).
`db`	`EnsDb` object.
`with.tables`	optional `character` vector specifying the names of the database tables that are being queried.

Value

A character(1) with the SQL where condition.

Note

This function might be used in direct SQL queries on the SQLite database underlying an EnsDb but is more thought to illustrate the use of AnnotationFilter objects in combination with SQL databases. This method is used internally to create the SQL calls to the database.

Author(s)

Johannes Rainer

Examples

library(EnsDb.Hsapiens.v86)
edb <- EnsDb.Hsapiens.v86

## Define a filter
flt <- AnnotationFilter(~ gene_name == "BCL2")

## Use the method from the AnnotationFilter package:
convertFilter(flt)

## Create a combination of filters
flt_list <- AnnotationFilter(~ gene_name %in% c("BCL2", "BCL2L11") &
    tx_biotype == "protein_coding")
flt_list

convertFilter(flt_list)

## Use the filters in the context of an EnsDb database:
convertFilter(flt, edb)

convertFilter(flt_list, edb)

ensembldb

Utilities to create and use Ensembl-based annotation databases

v2.14.1

LGPL

Authors

Johannes Rainer <johannes.rainer@eurac.edu> with contributions from Tim Triche, Sebastian Gibb, Laurent Gatto and Christian Weichenberger.

Initial release