Filters for annotation objects
The filters extending the base AnnotationFilter class
represent a simple filtering concept for annotation resources.
Each filter object is thought to filter on a single (database)
table column using the provided values and the defined condition.
Filter instances created using the constructor functions (e.g.
GeneIdFilter).
supportedFilters() lists all defined filters. It returns a two column
data.frame with the filter class name and its default field.
Packages using AnnotationFilter should implement the
supportedFilters for their annotation resource object (e.g. for
object = "EnsDb" in the ensembldb package) to list all
supported filters for the specific resource.
condition() get the condition value for
the filter object.
value() get the value for the filter
object.
field() get the field for the filter
object.
not() get the not for the filter object.
feature() get the feature for the
GRangesFilter object.
Converts an AnnotationFilter object to a
character(1) giving an equation that can be used as input to
a dplyr filter.
AnnotationFilter translates a filter
expression such as ~ gene_id == "BCL2" into a filter object
extending the AnnotationFilter class (in the example a
GeneIdFilter object) or an
AnnotationFilterList if the expression contains multiple
conditions (see examples below). Filter expressions have to be written
in the form ~ <field> <condition> <value>, with <field>
being the default field of the filter class (use the
supportedFilter function to list all fields and filter classes),
<condition> the logical expression and <value> the value
for the filter.
CdsStartFilter(value, condition = "==", not = FALSE)
CdsEndFilter(value, condition = "==", not = FALSE)
ExonIdFilter(value, condition = "==", not = FALSE)
ExonNameFilter(value, condition = "==", not = FALSE)
ExonRankFilter(value, condition = "==", not = FALSE)
ExonStartFilter(value, condition = "==", not = FALSE)
ExonEndFilter(value, condition = "==", not = FALSE)
GeneIdFilter(value, condition = "==", not = FALSE)
GeneNameFilter(value, condition = "==", not = FALSE)
GeneBiotypeFilter(value, condition = "==", not = FALSE)
GeneStartFilter(value, condition = "==", not = FALSE)
GeneEndFilter(value, condition = "==", not = FALSE)
EntrezFilter(value, condition = "==", not = FALSE)
SymbolFilter(value, condition = "==", not = FALSE)
TxIdFilter(value, condition = "==", not = FALSE)
TxNameFilter(value, condition = "==", not = FALSE)
TxBiotypeFilter(value, condition = "==", not = FALSE)
TxStartFilter(value, condition = "==", not = FALSE)
TxEndFilter(value, condition = "==", not = FALSE)
ProteinIdFilter(value, condition = "==", not = FALSE)
UniprotFilter(value, condition = "==", not = FALSE)
SeqNameFilter(value, condition = "==", not = FALSE)
SeqStrandFilter(value, condition = "==", not = FALSE)
## S4 method for signature 'AnnotationFilter'
condition(object)
## S4 method for signature 'AnnotationFilter'
value(object)
## S4 method for signature 'AnnotationFilter'
field(object)
## S4 method for signature 'AnnotationFilter'
not(object)
GRangesFilter(value, feature = "gene", type = c("any", "start", "end",
"within", "equal"))
feature(object)
## S4 method for signature 'AnnotationFilter,missing'
convertFilter(object)
## S4 method for signature 'missing'
supportedFilters(object)
AnnotationFilter(expr)object |
An |
value |
|
feature |
|
type |
|
expr |
A filter expression, written as a |
condition |
|
not |
|
By default filters are only available for tables containing the
field on which the filter acts (i.e. that contain a column with the
name matching the value of the field slot of the
object). See the vignette for a description to use filters for
databases in which the database table column name differs from the
default field of the filter.
Filter expressions for the AnnotationFilter class have to be
written as formulas, i.e. starting with a ~.
The constructor function return an object extending
AnnotationFilter. For the return value of the other methods see
the methods' descriptions.
character(1) that can be used as input to a dplyr
filter.
AnnotationFilter returns an
AnnotationFilter or an AnnotationFilterList.
Translation of nested filter expressions using the
AnnotationFilter function is not yet supported.
AnnotationFilterList for combining
AnnotationFilter objects.
## filter by GRanges
GRangesFilter(GenomicRanges::GRanges("chr10:87869000-87876000"))
## Create a SymbolFilter to filter on a gene's symbol.
sf <- SymbolFilter("BCL2")
sf
## Create a GeneStartFilter to filter based on the genes' chromosomal start
## coordinates
gsf <- GeneStartFilter(10000, condition = ">")
gsf
filter <- SymbolFilter("ADA", "==")
result <- convertFilter(filter)
result
supportedFilters()
## Convert a filter expression based on a gene ID to a GeneIdFilter
gnf <- AnnotationFilter(~ gene_id == "BCL2")
gnf
## Same conversion but for two gene IDs.
gnf <- AnnotationFilter(~ gene_id %in% c("BCL2", "BCL2L11"))
gnf
## Converting an expression that combines multiple filters. As a result we
## get an AnnotationFilterList containing the corresponding filters.
## Be aware that nesting of expressions/filters does not work.
flt <- AnnotationFilter(~ gene_id %in% c("BCL2", "BCL2L11") &
tx_biotype == "nonsense_mediated_decay" |
seq_name == "Y")
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