filter: Filtering src_organism objects

Description Usage Arguments Details Value Author(s) See Also Examples

Description

These functions create filters to be used by the "select" interface to src_organism objects.

Usage

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AccnumFilter(value, condition = "==")
AliasFilter(value, condition = "==")
CdsChromFilter(value, condition = "==")
CdsIdFilter(value, condition = "==")
CdsNameFilter(value, condition = "==")
CdsStrandFilter(value, condition = "==")
EnsemblFilter(value, condition = "==")
EnsemblprotFilter(value, condition = "==")
EnsembltransFilter(value, condition = "==")
EnzymeFilter(value, condition = "==")
EvidenceFilter(value, condition = "==")
EvidenceallFilter(value, condition = "==")
ExonChromFilter(value, condition = "==")
ExonStrandFilter(value, condition = "==")
FlybaseFilter(value, condition = "==")
FlybaseCgFilter(value, condition = "==")
FlybaseProtFilter(value, condition = "==")
GeneChromFilter(value, condition = "==")
GeneStrandFilter(value, condition = "==")
GoFilter(value, condition = "==")
GoallFilter(value, condition = "==")
IpiFilter(value, condition = "==")
MapFilter(value, condition = "==")
MgiFilter(value, condition = "==")
OmimFilter(value, condition = "==")
OntologyFilter(value, condition = "==")
OntologyallFilter(value, condition = "==")
PfamFilter(value, condition = "==")
PmidFilter(value, condition = "==")
PrositeFilter(value, condition = "==")
RefseqFilter(value, condition = "==")
TxChromFilter(value, condition = "==")
TxStrandFilter(value, condition = "==")
TxTypeFilter(value, condition = "==")
WormbaseFilter(value, condition = "==")
ZfinFilter(value, condition = "==")

## S4 method for signature 'BasicFilter'
show(object)

## S4 method for signature 'src_organism'
supportedFilters(object)

Arguments

object

A BasicFilter or GRangesFilter object

value

Value of the filter. For GRangesFilter value should be a GRanges object.

condition

The condition to be used in filter for genomic extractors, one of "==", "!=", "startsWith", "endsWith", ">", "<", ">=", "<=". For character values "==", "!=", "startsWith" and "endsWith" are allowed, for numeric values (CdsStartFilter, CdsEndFilter, ExonStartFilter, ExonEndFilter, GeneStartFilter, GeneEndFilter, TxStartFilter and TxEndFilter), "==", "!=", ">", ">=", "<" and "<=". Default condition is "==".

Details

All filters except GRangesFilter() takes value(s) from corresponding fields in the data base. For example, AccnumFilter() takes values of accession number(s), which come from field accnum. See keytypes() and keys() for possible values.

GRangesFilter() takes a GRanges object as filter, and returns genomic extractors (genes, transcripts, etc.) that are partially overlapping with the region.

supportedFilters() lists all available filters for src_organism object.

Value

A Filter object showing class, value and condition of the filter

Author(s)

Yubo Cheng.

See Also

src_organism for creating a src_organism object.

transcripts_tbl for generic functions to extract genomic features from a src_organism object.

select,src_organism-method for "select" interface on src_organism objects.

Examples

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src <- src_organism(dbpath=hg38light())
keytypes(src)
head(keys(src, "ensembl"))

## filter by ensembl
EnsemblFilter("ENSG00000171862")

## filter by gene symbol start with "BRAC"
SymbolFilter("BRCA", "startsWith")

## filter by GRanges
GRangesFilter(GenomicRanges::GRanges("chr10:87869000-87876000"))

## filter by transcript start position
TxStartFilter(87863438, ">")

Bioconductor/Organism.dplyr documentation built on May 22, 2021, 8:59 a.m.