Globally add filters to an EnsDb database
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.
## 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())
x |
The |
filter |
The filter as an
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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.
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.
Johannes Rainer
Filter-classes for a list of all supported filters.
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.