GeneidFilter-class: Filter results fetched from the Ensembl database

In jotsetung/ensembldb-old: Utilities to create and use an Ensembl based annotation database

Description

These classes allow to specify which entries (i.e. genes, transcripts or exons) should be retrieved from the database.

Details

ExonidFilter

Allows to filter based on the (Ensembl) exon identifier.

EntrezidFilter

Filter results based on the NCBI Entrezgene identifierts of the genes. Use the listGenebiotypes method to get a complete list of all available gene biotypes.

GenebiotypeFilter

Filter results based on the gene biotype as defined in the Ensembl database.

GeneidFilter

Filter results based on the Ensembl gene identifiers.

GenenameFilter

Allows to filter on the gene names (symbols) of the genes.

SeqendFilter

Filter based on the chromosomal end coordinate of the exons, transcripts or genes.

SeqnameFilter

Filter on the sequence name on which the features are encoded (mostly the chromosome names).

SeqstartFilter

Filter based on the chromosomal start coordinates of the exons, transcripts or genes.

SeqstrandFilter

Filter based on the strand on which the features are encoded.

TxbiotypeFilter

Filter on the transcript biotype defined in Ensembl. Use the listTxbiotypes method to get a complete list of all available transcript biotypes.

TxidFilter

Filter on the Ensembl transcript identifiers.

Objects from the Class

While objects can be created by calls e.g. of the form new("GeneidFilter", ...) users are strongly encouraged to use the specific functions: GeneidFilter, EntrezidFilter, GenenameFilter, GenebiotypeFilter, TxidFilter, TxbiotypeFilter, ExonidFilter, SeqnameFilter, SeqstrandFilter, SeqstartFilter and SeqendFilter. See examples below for usage.

Slots

condition:

Object of class "character": can be either "=", "in" or "like" to filter on character values (e.g. gene id, gene biotype, seqname etc), or "=", ">" or "<" for numerical values (chromosome/seq coordinates). Note that for "like" value should be a SQL pattern (e.g. "ENS%").

value:

Object of class "character": the value to be used for filtering.

Extends

Class BasicFilter, directly.

Methods

Note: these methods are applicable to all classes extending the BasicFilter class.

column

signature(object = "GeneidFilter", db="EnsDb", with.tables="character"): returns the column (attribute name) to be used for the filtering. Submitting the db parameter ensures that returned column is valid in the corresponding database schema. The optional argument with.tables allows to specify which in which database table the function should look for the attribute/column name. By default the method will check all database tables.

column

signature(object = "GeneidFilter", db="EnsDb", with.tables="missing"): returns the column (attribute name) to be used for the filtering. Submitting the db parameter ensures that returned column is valid in the corresponding database schema.

column

signature(object = "GeneidFilter", db="missing", with.tables="missing"): returns the column (table column name) to be used for the filtering.

condition

signature(x="BasicFilter"): returns the value for the condition slot.

where

signature(object = "GeneidFilter", db="EnsDb", with.tables="character"): returns the where clause for the SQL call. Submitting also the db parameter ensures that the columns are valid in the corresponding database schema. The optional argument with.tables allows to specify which in which database table the function should look for the attribute/column name. By default the method will check all database tables.

where

signature(object = "GeneidFilter", db="EnsDb", with.tables="missing"): returns the where clause for the SQL call. Submitting also the db parameter ensures that the columns are valid in the corresponding database schema.

where

signature(object = "GeneidFilter", db="missing", with.tables="missing"): returns the where clause for the SQL call.

Note

The column and where methods should be always called along with the EnsDb object, as this ensures that the returned column names are valid for the database schema. The optional argument with.tables should on the other hand only be used rarely as it is more intended for internal use.

Note that the database column "entrezid" queried for EntrezidFilter classes can contain multiple, ";" separated, Entrezgene IDs, thus, using this filter at present might not return all entries from the database.

Author(s)

Johannes Rainer

See Also

genes, transcripts, exons, listGenebiotypes, listTxbiotypes

Examples

## create a filter that could be used to retrieve all informations for
## the respective gene.
Gif <- GeneidFilter("ENSG00000012817")
Gif
## returns the where clause of the SQL querys
where(Gif)

## create a filter for a chromosomal end position of a gene
Sef <- SeqendFilter(10000, condition=">", "gene")
Sef

## for additional examples see the help page of "genes"

jotsetung/ensembldb-old documentation built on May 19, 2019, 9:41 p.m.