BasicFilter-class {Organism.dplyr} | R Documentation

## Filtering src_organism objects

### Description

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

### Usage

    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 = "==")
    UnigeneFilter(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

    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, ">")

[Package Organism.dplyr version 1.6.2 Index]