FilterConstructors: Constructor functions for filter objects

In jotsetung/mirhostgenes: mirhostgenes: putting miRNAs into genomic context

Description

These functions allow to create filter objects that can be used to retrieve specific elements from the annotation database.

Usage

AlignmentIdFilter(value, condition = "==")

ArrayFilter(value, condition = "==")

DatabaseFilter(value, condition = "==")

MatMirnaConfidence(value="high", condition="==")

MatMirnaFilter(value, condition = "==", match.case=TRUE)

MatMirnaIdFilter(value, condition = "==")

MirfamFilter(value, condition = "==", match.case=TRUE)

MirfamIdFilter(value, condition = "==")

PositionFilter(value, condition = "==")

PreMirnaConfidence(value="high", condition="==")

PreMirnaFilter(value, condition = "==", match.case=TRUE)

PreMirnaIdFilter(value, condition = "==")

ProbesetIdFilter(value, condition = "==")

ReadCountFilter(value=0, condition=">", of="pre_mirna")

Arguments

condition	The condition to be used in the comparison. For character values "=", "in" and "like" are allowed, for numeric values (SeqstartFilter and SeqendFilter) "=", ">", ">=", "<" and "<=". Note that for "like" value should be a SQL pattern (e.g. "ENS%").
match.case	For PreMirnaFilter, MatMirnaFilter and MirfamFilter: whether the query should be performed case sensitive or insensitive.
of	For ReadCountFilter: whether the read count filter should be applied to pre-miRNAs ("pre_mirna") or mature miRNAs ("mat_mirna").
value	The filter value, e.g., for GeneIdFilter the id of the feature for which the data should be retrieved. For PositionFilter either "exonic", "intronic" or "both" are allowed, specifying that the (pre-)miRNA should be located in an exon, intron or within a host transcript. Can be any string for PreMirnaFilter, PreMirnaIdFilter, MatMirnaFilter and MatMirnaIdFilter. For MatMirnaConfidence and PreMirnaConfidence at present only a value of "high" is allowed, which allows to retrieve pre-miRNAs or mature miRNAs specified as high confidence in the miRBase.

Value

Depending on the function called, an instance of: ArrayFilter, AlignmentIdFilter, DatabaseFilter, MatMirnaConfidence, MatMirnaFilter, MatMirnaIdFilter, MirfamFilter, MirfamIdFilter, PositionFilter, PreMirnaConfidence, PreMirnaFilter, PreMirnaIdFilter, ProbesetIdFilter, ReadCountFilter

Author(s)

Johannes Rainer

See Also

hostgenes, hosttx, ArrayFilter, AlignmentIdFilter, DatabaseFilter, PositionFilter, PreMirnaFilter, PreMirnaIdFilter, ProbesetIdFilter, MatMirnaFilter, MatMirnaIdFilter GeneIdFilter, GenenameFilter, GeneBiotypeFilter, TxIdFilter, TxBiotypeFilter, ExonIdFilter, SeqNameFilter, SeqStrandFilter

Examples

## Note: for additional examples see the help of the
## hostgenes, hosttx etc. functions.

library(MirhostDb.Hsapiens.v75.v20)

## create a filter that could be used to retrieve all host genes with
## a pre-miRNA encoded in one of their exons.
Pos <- PositionFilter("exonic")

where(Pos, MirhostDb.Hsapiens.v75.v20)
column(Pos, MirhostDb.Hsapiens.v75.v20)

## Next we define a SeqstartFilter (defined in the AnnotationFilter
## package)
Start <- SeqStartFilter(12333)

## the default where and column calls will return us the settings
## required for the makeEnsemblDb package
where(Start)
column(Start)

## however, that would not work in a mirhostgenes package since we're
## interested in the genomic alignment of miRNAs, not genes. Thus,
## submitting in addition the instance of the mirhostgenes database
## returns the correct columns and where clause:
Start <- SeqStartFilter(12333, feature="pre_mirna")
where(Start, MirhostDb.Hsapiens.v75.v20)
column(Start, MirhostDb.Hsapiens.v75.v20)

jotsetung/mirhostgenes documentation built on May 19, 2019, 9:42 p.m.