Filter-imported: Filters imported from ensembldb

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

Description

These filters are imported from the ensembldb package and can also be used to specify which entries (i.e. genes, transcripts) should be retrieved from the database.

Details

Description of filters (in alphabetical order).

GeneBiotypeFilter

Allows to filter on the biotype of the host gene. Use method listGenebiotypes to get an overview of the available choices.

GeneIdFilter

Allows to filter results based on the gene ID of the host gene.

GenenameFilter

Allows to filter results based on the gene name (symbol) of the host gene.

EntrezFilter

Allows to filter on the NCBI Entrezgene ID of the host gene.

TxBiotypeFilter

Allows to filter on the biotype of the host transcript. Use the method listTxbiotypes to get an overview of available choices.

TxIdFilter

Allows to filter on the transcript ID of the host gene.

ExonIdFilter

Filter results based on the ID of the exon in which a pre-miRNA is encoded (only for exonic miRNAs).

SeqEndFilter

Filter results based on the chromosomal end coordinate of mature miRNAs (if feature="mat_mirna") or pre-miRNAs (if feature="pre_mirna").

SeqNameFilter

Filter results based on the seqname (chromosome name) on which the miRNAs are encoded.

SeqStrandFilter

Filter results based on the strand on which the miRNAs are encoded.

SeqStartFilter

Filter results based on the chromosomal start coordinate of mature miRNAs (if feature="mat_mirna") or pre-miRNAs (if feature="pre_mirna").

Value

See method descriptions above for the return values.

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, GenenameFilter, GeneBiotypeFilter, EntrezFilter, TxIdFilter, ExonIdFilter, SeqNameFilter, SeqStrandFilter 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 "AnnotationFilter" defined in the AnnotationFilter package.

Methods

column

signature(object = "GeneIdFilter", db = "MirhostDb", with.tables="character"): returns the column (table column name in the miRNA host genes database) to be used for the filtering. The method can be applied to any filter class defined in the mirhostgenes or ensembldb packages. Argument with.tables allows to restrict the filter to be applied to certain database tables. By default the filter is applied to all database tables.

The method returns a character string with the name of the column.

where

signature(object = "GeneIdFilter", db = "MirhostDb", with.tables="character"): returns the where clause for the SQL call to the miRNA host genes database. The method can be applied to any filter class defined in the mirhostgenes or ensembldb packages. Argument with.tables allows to restrict the filter to be applied to certain database tables. By default the filter is applied to all database tables.

The method returns the SQL where clause that will be used to restrict the results returned by the database. This string is dependent on the type of database.

Author(s)

Johannes Rainer

See Also

GeneIdFilter, PreMirnaFilter

Examples

library(MirhostDb.Hsapiens.v75.v20)

## 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 specific for the
## mirhostgenes database
where(Gif, MirhostDb.Hsapiens.v75.v20)

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

## in the miRNA host genes database we are rather interested to get
## pre-miRNAs from certain genomic positions, thus we define "pre_mirna"
## as the feature and call where by supplying also the MirhostDb
## object
Sef <- SeqEndFilter(1000, condition=">", "pre_mirna")
where(Sef, MirhostDb.Hsapiens.v75.v20)

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