ensembldb (version 1.4.6)

GeneidFilter-class: Filter results fetched from the Ensembl database

Description

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

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, GRangesFilter, TxidFilter, TxbiotypeFilter, ExonidFilter, ExonrankFilter, SeqnameFilter, SeqstrandFilter, SeqstartFilter and SeqendFilter.

See examples below for usage.

Extends

Class BasicFilter, directly.

Details

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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 condition 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"


## Example for GRangesFilter:
## retrieve all genes overlapping the specified region
grf <- GRangesFilter(GRanges("11", ranges=IRanges(114000000, 114000050),
                             strand="+"), condition="overlapping")
library(EnsDb.Hsapiens.v75)
edb <- EnsDb.Hsapiens.v75
genes(edb, filter=grf)

## Get also all transcripts overlapping that region
transcripts(edb, filter=grf)

## Retrieve all transcripts for the above gene
gn <- genes(edb, filter=grf)
txs <- transcripts(edb, filter=GenenameFilter(gn$gene_name))
## Next we simply plot their start and end coordinates.
plot(3, 3, pch=NA, xlim=c(start(gn), end(gn)), ylim=c(0, length(txs)), yaxt="n", ylab="")
## Highlight the GRangesFilter region
rect(xleft=start(grf), xright=end(grf), ybottom=0, ytop=length(txs), col="red", border="red")
for(i in 1:length(txs)){
    current <- txs[i]
    rect(xleft=start(current), xright=end(current), ybottom=i-0.975, ytop=i-0.125, border="grey")
    text(start(current), y=i-0.5,pos=4, cex=0.75, labels=current$tx_id)
}
## Thus, we can see that only 4 transcripts of that gene are indeed overlapping the region.


## No exon is overlapping that region, thus we're not getting anything
exons(edb, filter=grf)


## Example for ExonrankFilter
## Extract all exons 1 and (if present) 2 for all genes encoded on the
## Y chromosome
exons(edb, columns=c("tx_id", "exon_idx"),
      filter=list(SeqnameFilter("Y"),
                  ExonrankFilter(3, condition="<")))