ensembldb (version 1.0.1)

SeqendFilter: Constructor functions for filter objects

Description

These functions allow to create filter objects that can be used to retrieve specific elements from the annotation database.

Usage

EntrezidFilter(value, condition = "=")
GeneidFilter(value, condition = "=")
GenenameFilter(value, condition = "=")
GenebiotypeFilter(value, condition = "=")
TxidFilter(value, condition = "=")
TxbiotypeFilter(value, condition = "=")
ExonidFilter(value, condition = "=")
SeqnameFilter(value, condition = "=")
SeqstrandFilter(value, condition = "=")
SeqstartFilter(value, condition = "=", feature = "gene")
SeqendFilter(value, condition = "=", feature = "gene")

Arguments

value

The filter value, e.g., for GeneidFilter the id of the gene for which the data should be retrieved. For character values (all filters except SeqstartFilter and SeqendFilter) also a character vector of values is allowed. Allowed values for SeqstrandFilter are: "+", "-", "1" or "-1".

condition

The condition to be used in the comparison. For character values "=", "in" and "like" are allowed, for numeric values (SeqstartFilter and SeqendFilter) "=", ">", ">=", "<"< code=""> and "<="< code="">. Note that for "like" value should be a SQL pattern (e.g. "ENS%").

feature

For SeqstartFilter and SeqendFilter: the chromosomal position of which features should be used in the filter (either "gene", "transcript" or "exon")?

Value

Depending on the function called an instance of: EntrezidFilter, GeneidFilter, GenenameFilter, GenebiotypeFilter, TxidFilter, TxbiotypeFilter, ExonidFilter, SeqnameFilter, SeqstrandFilter, SeqstartFilter, SeqendFilter

Details

EntrezidFilter

Filter results based on the NCBI Entrezgene ID of the genes.

GeneidFilter

Filter results based on Ensembl gene IDs.

GenenameFilter

Filter results based on gene names (gene symbols).

GenebiotypeFilter

Filter results based on the biotype of the genes. For a complete list of available gene biotypes use the listGenebiotypes method.

TxidFilter

Filter results based on the Ensembl transcript IDs.

TxbiotypeFilter

Filter results based on the biotype of the transcripts. For a complete list of available transcript biotypes use the listTxbiotypes method.

ExonidFilter

Filter based on the Ensembl exon ID.

SeqnameFilter

Filter results based on the name of the sequence the features are encoded.

SeqstrandFilter

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

SeqstartFilter

Filter results based on the (chromosomal) start coordinate of the features (exons, genes or transcripts).

SeqendFilter

Filter results based on the (chromosomal) end coordinates.

See Also

EntrezidFilter, GeneidFilter, GenenameFilter, GenebiotypeFilter, TxidFilter, TxbiotypeFilter, ExonidFilter, SeqnameFilter, SeqstrandFilter, SeqstartFilter, SeqendFilter

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(100000, condition="<", "gene")
Sef

## To find genes within a certain chromosomal position filters should be
## combined:
Ssf <- SeqstartFilter(10000, condition=">", "gene")
Snf <- SeqnameFilter("2")
## combine the filters
Filter <- list(Ssf, Sef, Snf)

Filter

## generate the where SQL call for these filters:
where(Filter)