BasicFilter-class {Organism.dplyr} | R Documentation |
These functions create filters to be used by the "select"
interface to src_organism
objects.
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)
object |
A |
value |
Value of the filter. For |
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
( |
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.
A Filter object showing class, value and condition of the filter
Yubo Cheng.
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.
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, ">")