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 = "=")
GRangesFilter(value, condition="within", feature="gene")
TxidFilter(value, condition = "=")
TxbiotypeFilter(value, condition = "=")
ExonidFilter(value, condition = "=")
ExonrankFilter(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".

For GRangeFilter this has to be a GRanges object.

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%").
    For GRangesFilter, "within" and "overlapping"
    are allowed. See below for details.

feature

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

For GRangesFilter: the submitted value is overwritten internally depending on the called method, i.e. calling genes will set feature to "gene", transcripts to "tx" and exons to "exon".

Value

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

Details

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Examples

Run this code

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


## Create a GRangesFilter
GRangesFilter(GRanges("X", IRanges(123, 5454)))

## Create a GRangesFilter with multiple ranges
grf <- GRangesFilter(GRanges(c("X", "Y"),
                             IRanges(start=c(123, 900),
                                     end=c(5454, 910))))
## Evaluate the "where" SQL where that would be applied.
where(grf)
## Change the "condition" of the filter and evaluate the
## where condition again.
condition(grf) <- "overlapping"
where(grf)