EnsDb-exonsBy.RdRetrieve gene/transcript/exons annotations stored in an Ensembl based
database package generated with the makeEnsembldbPackage
function. Parameter filter enables to define filters to
retrieve only specific data. Alternatively, a global filter might be
added to the EnsDb object using the addFilter
method.
# S4 method for EnsDb
exons(x, columns = listColumns(x,"exon"),
filter = AnnotationFilterList(), order.by,
order.type = "asc", return.type = "GRanges")
# S4 method for EnsDb
exonsBy(x, by = c("tx", "gene"),
columns = listColumns(x, "exon"), filter =
AnnotationFilterList(), use.names = FALSE)
# S4 method for EnsDb
intronsByTranscript(x, ..., use.names = FALSE)
# S4 method for EnsDb
exonsByOverlaps(x, ranges, maxgap = -1L, minoverlap = 0L,
type = c("any", "start", "end"), columns = listColumns(x, "exon"),
filter = AnnotationFilterList())
# S4 method for EnsDb
transcripts(x, columns = listColumns(x, "tx"),
filter = AnnotationFilterList(), order.by, order.type = "asc",
return.type = "GRanges")
# S4 method for EnsDb
transcriptsBy(x, by = c("gene", "exon"),
columns = listColumns(x, "tx"), filter = AnnotationFilterList())
# S4 method for EnsDb
transcriptsByOverlaps(x, ranges, maxgap = -1L,
minoverlap = 0L, type = c("any", "start", "end"),
columns = listColumns(x, "tx"), filter = AnnotationFilterList())
# S4 method for EnsDb
promoters(x, upstream = 2000, downstream = 200,
use.names = TRUE, ...)
# S4 method for EnsDb
genes(x, columns = c(listColumns(x, "gene"), "entrezid"),
filter = AnnotationFilterList(), order.by, order.type = "asc",
return.type = "GRanges")
# S4 method for EnsDb
cdsBy(x, by = c("tx", "gene"), columns = NULL,
filter = AnnotationFilterList(), use.names = FALSE)
# S4 method for EnsDb
fiveUTRsByTranscript(x, columns = NULL,
filter = AnnotationFilterList())
# S4 method for EnsDb
threeUTRsByTranscript(x, columns = NULL,
filter = AnnotationFilterList())
# S4 method for GRangesList
toSAF(x, ...)(In alphabetic order)
For promoters: additional arguments to be passed to the
transcripts method. For intronsByTranscript:
additional arguments such as filter.
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 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".
For method promoters: the number of nucleotides downstream of
the transcription start site that should be included in the promoter region.
A filter describing which results to retrieve from the database. Can
be a single object extending
AnnotationFilter, an
AnnotationFilterList object
combining several such objects or a formula representing a
filter expression (see examples below or
AnnotationFilter for more
details). Use the supportedFilters method to get an
overview of supported filter classes and related fields.
For exonsByOverlaps and transcriptsByOverlaps: see
exonsByOverlaps in GenomicFeatures for more
information.
For exonsByOverlaps and transcriptsByOverlaps: see
exonsByOverlaps in GenomicFeatures for more
information.
Character vector specifying the column(s) by which the result should
be ordered. This can be either in the form of
"gene_id, seq_name" or c("gene_id", "seq_name").
If the results should be ordered ascending
(asc, default) or descending (desc).
For exonsByOverlaps and transcriptsByOverlaps: a
GRanges object specifying the genomic regions.
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.
For exonsByOverlaps and transcriptsByOverlaps: see
exonsByOverlaps in GenomicFeatures for more
information.
For method promoters: the number of nucleotides upstream of
the transcription start site that should be included in the promoter region.
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.
Note that many methods and functions from the GenomicFeatures
package can also be used for EnsDb objects (such as
exonicParts,
intronicParts etc).
Retrieve exon information from the database. Additional columns from transcripts or genes associated with the exons can be specified and are added to the respective exon annotation.
Retrieve exons grouped by transcript or by gene. This
function returns a GRangesList as does the analogous function
in the GenomicFeatures package. Using the columns
parameter it is possible to determine which additional values should
be retrieved from the database. These will be included in the
GRanges object for the exons as metadata columns.
The exons in the inner GRanges are ordered by the exon
index within the transcript (if by="tx"), or increasingly by the
chromosomal start position of the exon or decreasingly by the chromosomal end
position of the exon depending whether the gene is encoded on the
+ or - strand (for by="gene").
The GRanges in the GRangesList will be ordered by
the name of the gene or transcript.
Retrieve introns by transcripts. Filters can also be passed to the
function. For more information see the intronsByTranscript
method in the GenomicFeatures package.
Retrieve exons overlapping specified genomic ranges. For
more information see the
exonsByOverlaps method in the
GenomicFeatures package. The functionality is to some
extent similar and redundant to the exons method in
combination with GRangesFilter filter.
Retrieve transcript information from the database. Additional columns from genes or exons associated with the transcripts can be specified and are added to the respective transcript annotation.
Retrieve transcripts grouped by gene or exon. This
function returns a GRangesList as does the analogous function
in the GenomicFeatures package. Using the columns
parameter it is possible to determine which additional values should
be retrieved from the database. These will be included in the
GRanges object for the transcripts as metadata columns.
The transcripts in the inner GRanges are ordered increasingly by the
chromosomal start position of the transcript for genes encoded on
the + strand and in a decreasing manner by the chromosomal end
position of the transcript for genes encoded on the - strand.
The GRanges in the GRangesList will be ordered by
the name of the gene or exon.
Retrieve transcripts overlapping specified genomic ranges. For
more information see
transcriptsByOverlaps method in the
GenomicFeatures package. The functionality is to some
extent similar and redundant to the transcripts method in
combination with GRangesFilter filter.
Retrieve promoter information from the database. Additional columns from genes or exons associated with the promoters can be specified and are added to the respective promoter annotation.
Retrieve gene information from the database. Additional columns
from transcripts or exons associated with the genes can be
specified and are added to the respective gene annotation. Note
that column "entrezid" is a list of Entrezgene
identifiers to accomodate the potential 1:n mapping between
Ensembl genes and Entrezgene IDs.
Returns the coding region grouped either by transcript or by
gene. Each element in the GRangesList represents the cds
for one transcript or gene, with the individual ranges
corresponding to the coding part of its exons.
For by="tx" additional annotation columns can be added to
the individual GRanges (in addition to the default columns
exon_id and exon_rank).
Note that the GRangesList is sorted by its names.
Returns the 5' untranslated region for protein coding transcripts.
Returns the 3' untranslated region for protein coding transcripts.
Reformats a GRangesList object into a
data.frame corresponding to a standard SAF (Simplified
Annotation Format) file (i.e. with column names "GeneID",
"Chr", "Start", "End" and
"Strand"). Note: this method makes only sense on a
GRangesList that groups features (exons, transcripts) by gene.
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:
the Ensembl gene ID of the gene.
the name of the gene (in most cases its official symbol).
the NCBI Entrezgene ID of the gene. Note that this
column contains a list of Entrezgene identifiers to
accommodate the potential 1:n mapping between Ensembl genes and
Entrezgene IDs.
the biotype of the gene.
the start coordinate of the gene on the sequence (usually a chromosome).
the end coordinate of the gene.
the name of the sequence the gene is encoded (usually a chromosome).
the strand on which the gene is encoded
the coordinate system of the sequence.
the Ensembl transcript ID.
the biotype of the transcript.
the chromosomal start coordinate of the transcript.
the chromosomal end coordinate of the transcript.
the start coordinate of the coding region of the transcript (NULL for non-coding transcripts).
the end coordinate of the coding region.
the G and C nucleotide content of the transcript's sequence expressed as a percentage (i.e. between 0 and 100).
the ID of the exon. In Ensembl, each exon specified by a unique chromosomal start and end position has its own ID. Thus, the same exon might be part of several transcripts.
the chromosomal start coordinate of the exon.
the chromosomal end coordinate of the exon.
the index of the exon in the transcript model. As noted above, an exon can be part of several transcripts and thus its position inside these transcript might differ.
Many EnsDb databases provide also protein related
annotations. See listProteinColumns for more information.
Ensembl defines genes not only on standard chromosomes, but also on
patched chromosomes and chromosome variants. Thus it might be
advisable to restrict the queries to just those chromosomes of
interest (e.g. by specifying a SeqNameFilter(c(1:22, "X", "Y"))).
In addition, also so called LRG genes (Locus Reference Genomic) are defined in
Ensembl. Their gene id starts with LRG instead of ENS for Ensembl
genes, thus, a filter can be applied to specifically select those
genes or exclude those genes (see examples below).
Depending on the value of the global option
"ucscChromosomeNames" (use
getOption(ucscChromosomeNames, FALSE) to get its value or
option(ucscChromosomeNames=TRUE) to change its value)
the sequence/chromosome names of the returned GRanges objects
or provided in the returned data.frame or DataFrame
correspond to Ensembl chromosome names (if value is FALSE) or
UCSC chromosome names (if TRUE). This ensures a better
integration with the Gviz package, in which this option is set
by default to TRUE.
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 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.
While it is possible to request values from a column "tx_name"
(with the columns argument), no such column is present in the
database. The returned values correspond to the ID of the transcripts.
supportedFilters to get an overview of supported filters.
makeEnsembldbPackage,
listColumns, lengthOf
addFilter for globally adding filters to an EnsDb
object.
library(EnsDb.Hsapiens.v86)
edb <- EnsDb.Hsapiens.v86
###### genes
##
## Get all genes encoded on chromosome Y
AllY <- genes(edb, filter = SeqNameFilter("Y"))
AllY
#> GRanges object with 523 ranges and 6 metadata columns:
#> seqnames ranges strand | gene_id
#> <Rle> <IRanges> <Rle> | <character>
#> ENSG00000251841 Y 2784749-2784853 + | ENSG00000251841
#> ENSG00000184895 Y 2786855-2787699 - | ENSG00000184895
#> ENSG00000237659 Y 2789827-2790328 + | ENSG00000237659
#> ENSG00000232195 Y 2827982-2828218 + | ENSG00000232195
#> ENSG00000129824 Y 2841486-2932000 + | ENSG00000129824
#> ... ... ... ... . ...
#> ENSG00000224240 Y 26549425-26549743 + | ENSG00000224240
#> ENSG00000227629 Y 26586642-26591601 - | ENSG00000227629
#> ENSG00000237917 Y 26594851-26634652 - | ENSG00000237917
#> ENSG00000231514 Y 26626520-26627159 - | ENSG00000231514
#> ENSG00000235857 Y 56855244-56855488 + | ENSG00000235857
#> gene_name gene_biotype seq_coord_system
#> <character> <character> <character>
#> ENSG00000251841 RNU6-1334P snRNA chromosome
#> ENSG00000184895 SRY protein_coding chromosome
#> ENSG00000237659 RNASEH2CP1 processed_pseudogene chromosome
#> ENSG00000232195 TOMM22P2 processed_pseudogene chromosome
#> ENSG00000129824 RPS4Y1 protein_coding chromosome
#> ... ... ... ...
#> ENSG00000224240 CYCSP49 processed_pseudogene chromosome
#> ENSG00000227629 SLC25A15P1 unprocessed_pseudogene chromosome
#> ENSG00000237917 PARP4P1 unprocessed_pseudogene chromosome
#> ENSG00000231514 FAM58CP processed_pseudogene chromosome
#> ENSG00000235857 CTBP2P1 processed_pseudogene chromosome
#> symbol entrezid
#> <character> <list>
#> ENSG00000251841 RNU6-1334P <NA>
#> ENSG00000184895 SRY 6736
#> ENSG00000237659 RNASEH2CP1 <NA>
#> ENSG00000232195 TOMM22P2 <NA>
#> ENSG00000129824 RPS4Y1 6192
#> ... ... ...
#> ENSG00000224240 CYCSP49 <NA>
#> ENSG00000227629 SLC25A15P1 <NA>
#> ENSG00000237917 PARP4P1 <NA>
#> ENSG00000231514 FAM58CP <NA>
#> ENSG00000235857 CTBP2P1 <NA>
#> -------
#> seqinfo: 1 sequence from GRCh38 genome
## Return the result as a DataFrame; also, we use a filter expression here
## to define which features to extract from the database.
AllY.granges <- genes(edb,
filter = ~ seq_name == "Y",
return.type="DataFrame")
AllY.granges
#> DataFrame with 523 rows and 10 columns
#> gene_id gene_name gene_biotype gene_seq_start
#> <character> <character> <character> <integer>
#> 1 ENSG00000251841 RNU6-1334P snRNA 2784749
#> 2 ENSG00000184895 SRY protein_coding 2786855
#> 3 ENSG00000237659 RNASEH2CP1 processed_pseudogene 2789827
#> 4 ENSG00000232195 TOMM22P2 processed_pseudogene 2827982
#> 5 ENSG00000129824 RPS4Y1 protein_coding 2841486
#> ... ... ... ... ...
#> 519 ENSG00000224240 CYCSP49 processed_pseudogene 26549425
#> 520 ENSG00000227629 SLC25A15P1 unprocessed_pseudogene 26586642
#> 521 ENSG00000237917 PARP4P1 unprocessed_pseudogene 26594851
#> 522 ENSG00000231514 FAM58CP processed_pseudogene 26626520
#> 523 ENSG00000235857 CTBP2P1 processed_pseudogene 56855244
#> gene_seq_end seq_name seq_strand seq_coord_system symbol entrezid
#> <integer> <character> <integer> <character> <character> <list>
#> 1 2784853 Y 1 chromosome RNU6-1334P NA
#> 2 2787699 Y -1 chromosome SRY 6736
#> 3 2790328 Y 1 chromosome RNASEH2CP1 NA
#> 4 2828218 Y 1 chromosome TOMM22P2 NA
#> 5 2932000 Y 1 chromosome RPS4Y1 6192
#> ... ... ... ... ... ... ...
#> 519 26549743 Y 1 chromosome CYCSP49 NA
#> 520 26591601 Y -1 chromosome SLC25A15P1 NA
#> 521 26634652 Y -1 chromosome PARP4P1 NA
#> 522 26627159 Y -1 chromosome FAM58CP NA
#> 523 56855488 Y 1 chromosome CTBP2P1 NA
## 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
#> GRanges object with 740 ranges and 5 metadata columns:
#> seqnames ranges strand | gene_id
#> <Rle> <IRanges> <Rle> | <character>
#> ENSG00000251841 Y 2784749-2784853 + | ENSG00000251841
#> ENSG00000184895 Y 2786855-2787699 - | ENSG00000184895
#> ENSG00000237659 Y 2789827-2790328 + | ENSG00000237659
#> ENSG00000232195 Y 2827982-2828218 + | ENSG00000232195
#> ENSG00000129824 Y 2841486-2932000 + | ENSG00000129824
#> ... ... ... ... . ...
#> ENSG00000224240 Y 26549425-26549743 + | ENSG00000224240
#> ENSG00000227629 Y 26586642-26591601 - | ENSG00000227629
#> ENSG00000237917 Y 26594851-26634652 - | ENSG00000237917
#> ENSG00000231514 Y 26626520-26627159 - | ENSG00000231514
#> ENSG00000235857 Y 56855244-56855488 + | ENSG00000235857
#> tx_id tx_biotype tx_seq_start
#> <character> <character> <integer>
#> ENSG00000251841 ENST00000516032 snRNA 2784749
#> ENSG00000184895 ENST00000383070 protein_coding 2786855
#> ENSG00000237659 ENST00000454281 processed_pseudogene 2789827
#> ENSG00000232195 ENST00000430735 processed_pseudogene 2827982
#> ENSG00000129824 ENST00000250784 protein_coding 2841486
#> ... ... ... ...
#> ENSG00000224240 ENST00000420810 processed_pseudogene 26549425
#> ENSG00000227629 ENST00000456738 unprocessed_pseudogene 26586642
#> ENSG00000237917 ENST00000435945 unprocessed_pseudogene 26594851
#> ENSG00000231514 ENST00000435741 processed_pseudogene 26626520
#> ENSG00000235857 ENST00000431853 processed_pseudogene 56855244
#> tx_seq_end
#> <integer>
#> ENSG00000251841 2784853
#> ENSG00000184895 2787699
#> ENSG00000237659 2790328
#> ENSG00000232195 2828218
#> ENSG00000129824 2867268
#> ... ...
#> ENSG00000224240 26549743
#> ENSG00000227629 26591601
#> ENSG00000237917 26634652
#> ENSG00000231514 26627159
#> ENSG00000235857 56855488
#> -------
#> seqinfo: 1 sequence from GRCh38 genome
###### transcripts
##
## Get all transcripts of a gene
Tx <- transcripts(edb,
filter = GeneIdFilter("ENSG00000184895"),
order.by = "tx_seq_start")
Tx
#> GRanges object with 1 range and 6 metadata columns:
#> seqnames ranges strand | tx_id
#> <Rle> <IRanges> <Rle> | <character>
#> ENST00000383070 Y 2786855-2787699 - | ENST00000383070
#> tx_biotype tx_cds_seq_start tx_cds_seq_end
#> <character> <integer> <integer>
#> ENST00000383070 protein_coding 2786989 2787603
#> gene_id tx_name
#> <character> <character>
#> ENST00000383070 ENSG00000184895 ENST00000383070
#> -------
#> seqinfo: 1 sequence from GRCh38 genome
## 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
#> GRanges object with 4 ranges and 6 metadata columns:
#> seqnames ranges strand | gene_id
#> <Rle> <IRanges> <Rle> | <character>
#> ENST00000383070 Y 2786855-2787699 - | ENSG00000184895
#> ENST00000383032 Y 6910686-7091683 + | ENSG00000092377
#> ENST00000355162 Y 6910686-7091683 + | ENSG00000092377
#> ENST00000346432 Y 6910686-7091683 + | ENSG00000092377
#> gene_seq_start gene_seq_end gene_biotype tx_biotype
#> <integer> <integer> <character> <character>
#> ENST00000383070 2786855 2787699 protein_coding protein_coding
#> ENST00000383032 6910686 7091683 protein_coding protein_coding
#> ENST00000355162 6910686 7091683 protein_coding protein_coding
#> ENST00000346432 6910686 7091683 protein_coding protein_coding
#> tx_id
#> <character>
#> ENST00000383070 ENST00000383070
#> ENST00000383032 ENST00000383032
#> ENST00000355162 ENST00000355162
#> ENST00000346432 ENST00000346432
#> -------
#> seqinfo: 1 sequence from GRCh38 genome
###### promoters
##
## Get the bona-fide promoters (2k up- to 200nt downstream of TSS)
promoters(edb, filter = GeneIdFilter(c("ENSG00000184895",
"ENSG00000092377")))
#> GRanges object with 4 ranges and 6 metadata columns:
#> seqnames ranges strand | tx_id
#> <Rle> <IRanges> <Rle> | <character>
#> ENST00000383070 Y 2787500-2789699 - | ENST00000383070
#> ENST00000383032 Y 6908686-6910885 + | ENST00000383032
#> ENST00000355162 Y 6908686-6910885 + | ENST00000355162
#> ENST00000346432 Y 6908686-6910885 + | ENST00000346432
#> tx_biotype tx_cds_seq_start tx_cds_seq_end
#> <character> <integer> <integer>
#> ENST00000383070 protein_coding 2786989 2787603
#> ENST00000383032 protein_coding 7025085 7091492
#> ENST00000355162 protein_coding 7025085 7091492
#> ENST00000346432 protein_coding 7025085 7091492
#> gene_id tx_name
#> <character> <character>
#> ENST00000383070 ENSG00000184895 ENST00000383070
#> ENST00000383032 ENSG00000092377 ENST00000383032
#> ENST00000355162 ENSG00000092377 ENST00000355162
#> ENST00000346432 ENSG00000092377 ENST00000346432
#> -------
#> seqinfo: 1 sequence from GRCh38 genome
###### exons
##
## Get all exons of protein coding transcript for the gene ENSG00000184895
Exon <- exons(edb,
filter = ~ gene_id == "ENSG00000184895" &
tx_biotype == "protein_coding",
columns = c("gene_id", "gene_seq_start", "gene_seq_end",
"tx_biotype", "gene_biotype"))
Exon
#> GRanges object with 1 range and 6 metadata columns:
#> seqnames ranges strand | gene_id
#> <Rle> <IRanges> <Rle> | <character>
#> ENSE00001494622 Y 2786855-2787699 - | ENSG00000184895
#> gene_seq_start gene_seq_end tx_biotype gene_biotype
#> <integer> <integer> <character> <character>
#> ENSE00001494622 2786855 2787699 protein_coding protein_coding
#> exon_id
#> <character>
#> ENSE00001494622 ENSE00001494622
#> -------
#> seqinfo: 1 sequence from GRCh38 genome
##### exonsBy
##
## Get all exons for transcripts encoded on chromosomes X and Y.
ETx <- exonsBy(edb, by = "tx",
filter = SeqNameFilter(c("X", "Y")))
ETx
#> GRangesList object of length 6829:
#> $ENST00000014935
#> GRanges object with 9 ranges and 2 metadata columns:
#> seqnames ranges strand | exon_id exon_rank
#> <Rle> <IRanges> <Rle> | <character> <integer>
#> [1] X 154409418-154410039 - | ENSE00001050512 1
#> [2] X 154409112-154409196 - | ENSE00001050508 2
#> [3] X 154405434-154405655 - | ENSE00001450968 3
#> [4] X 154404995-154405083 - | ENSE00000678418 4
#> [5] X 154404828-154404914 - | ENSE00003790806 5
#> [6] X 154403522-154403622 - | ENSE00000678413 6
#> [7] X 154403269-154403381 - | ENSE00003549633 7
#> [8] X 154402942-154403190 - | ENSE00000678409 8
#> [9] X 154401758-154402841 - | ENSE00001200781 9
#> -------
#> seqinfo: 2 sequences from GRCh38 genome
#>
#> ...
#> <6828 more elements>
## 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
#> GRangesList object of length 2922:
#> $ENSG00000000003
#> GRanges object with 20 ranges and 3 metadata columns:
#> seqnames ranges strand | gene_biotype gene_name
#> <Rle> <IRanges> <Rle> | <character> <character>
#> [1] X 100639945-100639991 - | protein_coding TSPAN6
#> [2] X 100636793-100637104 - | protein_coding TSPAN6
#> [3] X 100636608-100636806 - | protein_coding TSPAN6
#> [4] X 100636191-100636689 - | protein_coding TSPAN6
#> [5] X 100635558-100635746 - | protein_coding TSPAN6
#> ... ... ... ... . ... ...
#> [16] X 100632541-100632568 - | protein_coding TSPAN6
#> [17] X 100632063-100632068 - | protein_coding TSPAN6
#> [18] X 100630759-100630866 - | protein_coding TSPAN6
#> [19] X 100628670-100629986 - | protein_coding TSPAN6
#> [20] X 100627109-100629986 - | protein_coding TSPAN6
#> exon_id
#> <character>
#> [1] ENSE00001828996
#> [2] ENSE00001863395
#> [3] ENSE00001855382
#> [4] ENSE00001886883
#> [5] ENSE00003662440
#> ... ...
#> [16] ENSE00001849132
#> [17] ENSE00003731560
#> [18] ENSE00000868868
#> [19] ENSE00001459322
#> [20] ENSE00003730948
#> -------
#> seqinfo: 2 sequences from GRCh38 genome
#>
#> ...
#> <2921 more elements>
## Note that this might also contain "LRG" genes.
length(grep(names(EGenes), pattern="LRG"))
#> [1] 40
## to fetch just Ensemblgenes, use an GeneIdFilter with value
## "ENS%" and condition "like"
eg <- exonsBy(edb, by = "gene",
filter = AnnotationFilterList(SeqNameFilter(c("X", "Y")),
GeneIdFilter("ENS", "startsWith")),
columns = c("gene_biotype", "gene_name"))
eg
#> GRangesList object of length 2882:
#> $ENSG00000000003
#> GRanges object with 20 ranges and 4 metadata columns:
#> seqnames ranges strand | gene_biotype gene_name
#> <Rle> <IRanges> <Rle> | <character> <character>
#> [1] X 100639945-100639991 - | protein_coding TSPAN6
#> [2] X 100636793-100637104 - | protein_coding TSPAN6
#> [3] X 100636608-100636806 - | protein_coding TSPAN6
#> [4] X 100636191-100636689 - | protein_coding TSPAN6
#> [5] X 100635558-100635746 - | protein_coding TSPAN6
#> ... ... ... ... . ... ...
#> [16] X 100632541-100632568 - | protein_coding TSPAN6
#> [17] X 100632063-100632068 - | protein_coding TSPAN6
#> [18] X 100630759-100630866 - | protein_coding TSPAN6
#> [19] X 100628670-100629986 - | protein_coding TSPAN6
#> [20] X 100627109-100629986 - | protein_coding TSPAN6
#> exon_id gene_id
#> <character> <character>
#> [1] ENSE00001828996 ENSG00000000003
#> [2] ENSE00001863395 ENSG00000000003
#> [3] ENSE00001855382 ENSG00000000003
#> [4] ENSE00001886883 ENSG00000000003
#> [5] ENSE00003662440 ENSG00000000003
#> ... ... ...
#> [16] ENSE00001849132 ENSG00000000003
#> [17] ENSE00003731560 ENSG00000000003
#> [18] ENSE00000868868 ENSG00000000003
#> [19] ENSE00001459322 ENSG00000000003
#> [20] ENSE00003730948 ENSG00000000003
#> -------
#> seqinfo: 2 sequences from GRCh38 genome
#>
#> ...
#> <2881 more elements>
length(grep(names(eg), pattern="LRG"))
#> [1] 0
##### transcriptsBy
##
TGenes <- transcriptsBy(edb, by = "gene",
filter = SeqNameFilter(c("X", "Y")))
TGenes
#> GRangesList object of length 2922:
#> $ENSG00000000003
#> GRanges object with 5 ranges and 6 metadata columns:
#> seqnames ranges strand | tx_id
#> <Rle> <IRanges> <Rle> | <character>
#> [1] X 100633442-100639991 - | ENST00000494424
#> [2] X 100627109-100637104 - | ENST00000612152
#> [3] X 100632063-100637104 - | ENST00000614008
#> [4] X 100628670-100636806 - | ENST00000373020
#> [5] X 100632541-100636689 - | ENST00000496771
#> tx_biotype tx_cds_seq_start tx_cds_seq_end gene_id
#> <character> <integer> <integer> <character>
#> [1] processed_transcript <NA> <NA> ENSG00000000003
#> [2] protein_coding 100630798 100635569 ENSG00000000003
#> [3] protein_coding 100632063 100635569 ENSG00000000003
#> [4] protein_coding 100630798 100636694 ENSG00000000003
#> [5] processed_transcript <NA> <NA> ENSG00000000003
#> tx_name
#> <character>
#> [1] ENST00000494424
#> [2] ENST00000612152
#> [3] ENST00000614008
#> [4] ENST00000373020
#> [5] ENST00000496771
#> -------
#> seqinfo: 2 sequences from GRCh38 genome
#>
#> $ENSG00000000005
#> GRanges object with 2 ranges and 6 metadata columns:
#> seqnames ranges strand | tx_id
#> <Rle> <IRanges> <Rle> | <character>
#> [1] X 100584802-100599885 + | ENST00000373031
#> [2] X 100593624-100597531 + | ENST00000485971
#> tx_biotype tx_cds_seq_start tx_cds_seq_end gene_id
#> <character> <integer> <integer> <character>
#> [1] protein_coding 100585019 100599717 ENSG00000000005
#> [2] processed_transcript <NA> <NA> ENSG00000000005
#> tx_name
#> <character>
#> [1] ENST00000373031
#> [2] ENST00000485971
#> -------
#> seqinfo: 2 sequences from GRCh38 genome
#>
#> $ENSG00000001497
#> GRanges object with 5 ranges and 6 metadata columns:
#> seqnames ranges strand | tx_id
#> <Rle> <IRanges> <Rle> | <character>
#> [1] X 65512583-65534775 - | ENST00000484069
#> [2] X 65512582-65534756 - | ENST00000374811
#> [3] X 65512583-65534756 - | ENST00000374804
#> [4] X 65512582-65534754 - | ENST00000374807
#> [5] X 65520429-65523617 - | ENST00000469091
#> tx_biotype tx_cds_seq_start tx_cds_seq_end gene_id
#> <character> <integer> <integer> <character>
#> [1] nonsense_mediated_de.. 65525021 65534715 ENSG00000001497
#> [2] protein_coding 65512775 65534715 ENSG00000001497
#> [3] protein_coding 65512775 65534715 ENSG00000001497
#> [4] protein_coding 65512775 65534715 ENSG00000001497
#> [5] protein_coding 65520655 65523617 ENSG00000001497
#> tx_name
#> <character>
#> [1] ENST00000484069
#> [2] ENST00000374811
#> [3] ENST00000374804
#> [4] ENST00000374807
#> [5] ENST00000469091
#> -------
#> seqinfo: 2 sequences from GRCh38 genome
#>
#> ...
#> <2919 more elements>
## convert this to a SAF formatted data.frame that can be used by the
## featureCounts function from the Rsubreader package.
head(toSAF(TGenes))
#> GeneID Chr Start End Strand
#> 1 ENSG00000000003 X 100633442 100639991 -
#> 2 ENSG00000000003 X 100627109 100637104 -
#> 3 ENSG00000000003 X 100632063 100637104 -
#> 4 ENSG00000000003 X 100628670 100636806 -
#> 5 ENSG00000000003 X 100632541 100636689 -
#> 6 ENSG00000000005 X 100584802 100599885 +
##### 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
#> GRanges object with 0 ranges and 6 metadata columns:
#> seqnames ranges strand | tx_id tx_biotype tx_cds_seq_start
#> <Rle> <IRanges> <Rle> | <character> <character> <integer>
#> tx_cds_seq_end gene_id tx_name
#> <integer> <character> <character>
#> -------
#> seqinfo: 1 sequence from GRCh38 genome
## Alternatively, use a GRangesFilter
grf <- GRangesFilter(gr, type = "any")
txs <- transcripts(edb, filter = grf)
txs
#> GRanges object with 0 ranges and 6 metadata columns:
#> seqnames ranges strand | tx_id tx_biotype tx_cds_seq_start
#> <Rle> <IRanges> <Rle> | <character> <character> <integer>
#> tx_cds_seq_end gene_id tx_name
#> <integer> <character> <character>
#> -------
#> seqinfo: no sequences
#### 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")