exonsBy: Retrieve annotation data from an Ensembl based package

Description

Retrieve gene/transcript/exons annotations stored in an Ensembl based database package generated with the makeEnsembldbPackage function.

Usage

## S3 method for class 'EnsDb':
exons(x, columns=listColumns(x,"exon"),
                        filter, order.by, order.type="asc",
                        return.type="GRanges")
## S3 method for class 'EnsDb':
exonsBy(x, by=c("tx", "gene"),
                          columns=listColumns(x, "exon"), filter, use.names=FALSE)
## S3 method for class 'EnsDb':
exonsByOverlaps(x, ranges, maxgap=0L, minoverlap=1L,
                                  type=c("any", "start", "end"),
                                  columns=listColumns(x, "exon"),
                                  filter)
## S3 method for class 'EnsDb':
transcripts(x, columns=listColumns(x, "tx"),
                              filter, order.by, order.type="asc",
                              return.type="GRanges")
## S3 method for class 'EnsDb':
transcriptsBy(x, by=c("gene", "exon"),
                                columns=listColumns(x, "tx"), filter)
## S3 method for class 'EnsDb':
transcriptsByOverlaps(x, ranges, maxgap=0L, minoverlap=1L,
                                        type=c("any", "start", "end"),
                                        columns=listColumns(x, "tx"),
                                        filter)
## S3 method for class 'EnsDb':
promoters(x, upstream=2000, downstream=200, ...)
## S3 method for class 'EnsDb':
genes(x, columns=listColumns(x, "gene"), filter,
                        order.by, order.type="asc",
                        return.type="GRanges")
## S3 method for class 'EnsDb':
disjointExons(x, aggregateGenes=FALSE,
                                includeTranscripts=TRUE, filter, ...)
## S3 method for class 'EnsDb':
cdsBy(x, by=c("tx", "gene"), columns=NULL, filter,
                        use.names=FALSE)
## S3 method for class 'EnsDb':
fiveUTRsByTranscript(x, columns=NULL, filter)
## S3 method for class 'EnsDb':
threeUTRsByTranscript(x, columns=NULL, filter)
## S3 method for class 'GRangesList':
toSAF(x, ...)

Arguments

...

For promoters: additional arguments to be passed to the transcripts method.

aggregateGenes

For disjointExons: When FALSE (default) exon fragments that overlap multiple genes are dropped. When TRUE, all fragments are kept and the gene_id metadata column includes all gene IDs that overlap the exon fragment.

For exonsBy: wheter exons sould be fetched by genes or by transcripts; as in the corresponding function of the GenomicFeatures package. For transcriptsBy: whether transcripts should be fetched by genes or by exons; fetching transcripts by cds as supported by the transcriptsBy method in the GenomicFeatures package is currently not implemented. For cdsBy: whether cds should be fetched by transcript of by gene.

columns

Columns to be retrieved from the database tables.

Default values for genes are all columns from the gene database table, for exons and exonsBy the column names of the exon database table table and for transcript and transcriptBy the columns of the tx data base table (see details below for more information).

Note that any of the column names of the database tables can be submitted to any of the methods (use listTables or listColumns methods for a complete list of allowed column names).

For cdsBy: this argument is only supported for for by="tx".

downstream

For method promoters: the number of nucleotides downstream of the transcription start site that should be included in the promoter region.

filter

A filter object extending BasicFilter or a list of such object(s) to select specific entries from the database (see examples below).

includeTranscripts

For disjointExons: When TRUE (default) a tx_name metadata column is included that lists all transcript IDs that overlap the exon fragment. Note: this is different to the disjointExons function in the GenomicFeatures package, that lists the transcript names, not IDs.

maxgap

For exonsByOverlaps and transcriptsByOverlaps: see exonsByOverlaps help page in the GenomicFeatures package.

minoverlap

For exonsByOverlaps and transcriptsByOverlaps: see exonsByOverlaps help page in the GenomicFeatures package.

order.by

Name of one of the columns above on which the results should be sorted.

order.type

If the results should be ordered ascending (asc, default) or descending (desc).

ranges

For exonsByOverlaps and transcriptsByOverlaps: a GRanges object specifying the genomic regions.

return.type

Type of the returned object. Can be either "data.frame", "DataFrame" or "GRanges". In the latter case the return object will be a GRanges object with the GRanges specifying the chromosomal start and end coordinates of the feature (gene, transcript or exon, depending whether genes, transcripts or exons was called). All additional columns are added as metadata columns to the GRanges object.

type

For exonsByOverlaps and transcriptsByOverlaps: see exonsByOverlaps help page in the GenomicFeatures package.

upstream

For method promoters: the number of nucleotides upstream of the transcription start site that should be included in the promoter region.

use.names

For cdsBy and exonsBy: only for by="gene": use the names of the genes instead of their IDs as names of the resulting GRangesList.

For toSAF a GRangesList object. For all other methods an EnsDb instance.

Value

For exons, transcripts and genes, a data.frame, DataFrame or a GRanges, depending on the value of the return.type parameter. The result is ordered as specified by the parameter order.by or, if not provided, by seq_name and chromosomal start coordinate, but NOT by any ordering of values in eventually submitted filter objects.
For exonsBy, transcriptsBy: a GRangesList, depending on the value of the return.type parameter. The results are ordered by the value of the by parameter.
For exonsByOverlaps and transcriptsByOverlaps: a GRanges with the exons or transcripts overlapping the specified regions.
For toSAF: a data.frame with column names "GeneID" (the group name from the GRangesList, i.e. the ID by which the GRanges are split), "Chr" (the seqnames from the GRanges), "Start" (the start coordinate), "End" (the end coordinate) and "Strand" (the strand).
For disjointExons: a GRanges of non-overlapping exon parts.
For cdsBy: a GRangesList with GRanges per either transcript or exon specifying the start and end coordinates of the coding region of the transcript or gene.
For fiveUTRsByTranscript: a GRangesList with GRanges for each protein coding transcript representing the start and end coordinates of full or partial exons that constitute the 5' untranslated region of the transcript.
For threeUTRsByTranscript: a GRangesList with GRanges for each protein coding transcript representing the start and end coordinates of full or partial exons that constitute the 3' untranslated region of the transcript.

Details

A detailed description of all database tables and the associated attributes/column names is also given in the vignette of this package. An overview of the columns is given below: [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],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Also, the vignette provides examples on how to retrieve sequences for genes/transcripts/exons.

Examples

Run this code

library(EnsDb.Hsapiens.v75)
edb <- EnsDb.Hsapiens.v75

######   genes
##
## get all genes endcoded on chromosome Y
AllY <- genes(edb, filter=SeqnameFilter("Y"))
AllY

## return result as DataFrame.
AllY.granges <- genes(edb,
                      filter=SeqnameFilter("Y"),
                      return.type="DataFrame")
AllY.granges

## include all transcripts of the gene and their chromosomal
## coordinates, sort by chrom start of transcripts and return as
## GRanges.
AllY.granges.tx <- genes(edb,
                         filter=SeqnameFilter("Y"),
                         columns=c("gene_id", "seq_name",
                             "seq_strand", "tx_id", "tx_biotype",
                             "tx_seq_start", "tx_seq_end"),
                         order.by="tx_seq_start")
AllY.granges.tx



######   transcripts
##
## get all transcripts of a gene
Tx <- transcripts(edb,
                  filter=GeneidFilter("ENSG00000184895"),
                  order.by="tx_seq_start")
Tx

## get all transcripts of two genes along with some information on the
## gene and transcript
Tx <- transcripts(edb,
                  filter=GeneidFilter(c("ENSG00000184895",
                      "ENSG00000092377")),
                      columns=c("gene_id", "gene_seq_start",
                          "gene_seq_end", "gene_biotype", "tx_biotype"))
Tx

######   promoters
##
## get the bona-fide promoters (2k up- to 200nt downstream of TSS)
promoters(edb, filter=GeneidFilter(c("ENSG00000184895",
                                     "ENSG00000092377")))

######   exons
##
## get all exons of the provided genes
Exon <- exons(edb,
              filter=GeneidFilter(c("ENSG00000184895",
                  "ENSG00000092377")),
              order.by="exon_seq_start",
              columns=c( "gene_id", "gene_seq_start",
                  "gene_seq_end", "gene_biotype"))
Exon



#####    exonsBy
##
## get all exons for transcripts encoded on chromosomes X and Y.
ETx <- exonsBy(edb, by="tx",
               filter=SeqnameFilter(c("X", "Y")))
ETx
## get all exons for genes encoded on chromosome 1 to 22, X and Y and
## include additional annotation columns in the result
EGenes <- exonsBy(edb, by="gene",
                  filter=SeqnameFilter(c("X", "Y")),
                  columns=c("gene_biotype", "gene_name"))
EGenes

## Note that this might also contain "LRG" genes.
length(grep(names(EGenes), pattern="LRG"))

## to fetch just Ensemblgenes, use an GeneidFilter with value
## "ENS%" and condition "like"


#####    transcriptsBy
##
TGenes <- transcriptsBy(edb, by="gene",
                        filter=SeqnameFilter(c("X", "Y")))
TGenes

## convert this to a SAF formatted data.frame that can be used by the
## featureCounts function from the Rsubreader package.
head(toSAF(TGenes))


#####   transcriptsByOverlaps
##
ir <- IRanges(start=c(2654890, 2709520, 28111770),
              end=c(2654900, 2709550, 28111790))
gr <- GRanges(rep("Y", length(ir)), ir)

## Retrieve all transcripts overlapping any of the regions.
txs <- transcriptsByOverlaps(edb, gr)
txs

## Alternatively, use a GRangesFilter
grf <- GRangesFilter(gr, condition="overlapping")
txs <- transcripts(edb, filter=grf)
txs


####    cdsBy
## Get the coding region for all transcripts on chromosome Y.
## Specifying also additional annotation columns (in addition to the default
## exon_id and exon_rank).
cds <- cdsBy(edb, by="tx", filter=SeqnameFilter("Y"),
             columns=c("tx_biotype", "gene_name"))

####    the 5' untranslated regions:
fUTRs <- fiveUTRsByTranscript(edb, filter=SeqnameFilter("Y"))

####    the 3' untranslated regions with additional column gene_name.
tUTRs <- threeUTRsByTranscript(edb, filter=SeqnameFilter("Y"),
                               columns="gene_name")

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Description

Usage

Arguments

Value

Details

See Also

Examples