global-filters: Globally add filters to an EnsDb database

In jorainer/ensembldb: Utilities to create and use Ensembl-based annotation databases

Globally add filters to an EnsDb database

Description

These methods allow to set, delete or show globally defined filters on an EnsDb object.

addFilter: adds an annotation filter to the EnsDb object.

dropFilter deletes all globally set filters from the EnsDb object.

activeFilter returns the globally set filter from an EnsDb object.

filter filters an EnsDb object. filter is an alias for the addFilter function.

Usage

## S4 method for signature 'EnsDb'
addFilter(x, filter = AnnotationFilterList())

## S4 method for signature 'EnsDb'
dropFilter(x)

## S4 method for signature 'EnsDb'
activeFilter(x)

filter(x, filter = AnnotationFilterList())

Arguments

x	The EnsDb object to which the filter should be added.
filter	The filter as an AnnotationFilter, AnnotationFilterList or filter expression. See

Details

Adding a filter to an EnsDb object causes this filter to be permanently active. The filter will be used for all queries to the database and is added to all additional filters passed to the methods such as genes.

Value

addFilter and filter return an EnsDb object with the specified filter added.

activeFilter returns an AnnotationFilterList object being the active global filter or NA if no filter was added.

dropFilter returns an EnsDb object with all eventually present global filters removed.

Author(s)

Johannes Rainer

See Also

Filter-classes for a list of all supported filters.

Examples

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

## Add a global SeqNameFilter to the database such that all subsequent
## queries will be applied on the filtered database.
edb_y <- addFilter(edb, SeqNameFilter("Y"))

## Note: using the filter function is equivalent to a call to addFilter.

## Each call returns now only features encoded on chromosome Y
gns <- genes(edb_y)

seqlevels(gns)

## Get all lincRNA gene transcripts on chromosome Y
transcripts(edb_y, filter = ~ gene_biotype == "lincRNA")

## Get the currently active global filter:
activeFilter(edb_y)

## Delete this filter again.
edb_y <- dropFilter(edb_y)

activeFilter(edb_y)

jorainer/ensembldb documentation built on Aug. 23, 2024, 1:16 p.m.